Note: Descriptions are shown in the official language in which they were submitted.
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
POLYPEPTIDES HAVING CELLOBIOHYDROLASE ACTIVITY
AND POLYNUCLEOTIDES ENCODING SAME
Reference to a Sequence Listing
This application contains a Sequence Listing in computer readable form, which
is
incorporated herein by reference.
Reference to a Deposit of Biological Material
This application contains a reference to a deposit of biological material,
which deposit
is incorporated herein by reference.
Background of the Invention
Field of the Invention
The present invention relates to polypeptides having cellobiohydrolase
activity and
polynucleotides encoding the polypeptides. The invention also relates to
nucleic acid
constructs, vectors, and host cells comprising the polynucleotides as well as
methods of
producing and using the polypeptides.
Description of the Related Art
Cellulose is a polymer of the simple sugar glucose linked by beta-1,4 bonds.
Many
microorganisms produce enzymes that hydrolyze beta-linked glucans. These
enzymes
include endoglucanases, cellobiohydrolases, and beta-glucosidases.
Endoglucanases digest
the cellulose polymer at random locations, opening it to attack by
cellobiohydrolases.
Cellobiohydrolases sequentially release molecules of cellobiose from the ends
of the
cellulose polymer. Cellobiose is a water-soluble beta-1,4-linked dimer of
glucose. Beta-
glucosidases hydrolyze cellobiose to glucose.
The conversion of lignocellulosic feedstocks into ethanol has the advantages
of the
ready availability of large amounts of feedstock, the desirability of avoiding
burning or land
filling the materials, and the cleanliness of the ethanol fuel. Wood,
agricultural residues,
herbaceous crops, and municipal solid wastes have been considered as
feedstocks for
ethanol production. These materials primarily consist of cellulose,
hemicellulose, and lignin.
Once the cellulose is converted to glucose, the glucose is easily fermented by
yeast into
ethanol.
WO 2008/095033 discloses a fungal glycoside hydrolase.
It would be advantageous in the art to improve the ability to enzymatically
degrade
lignocellulosic feedstocks.
The present invention provides polypeptides having cellobiohydrolase activity
and
-1-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
polynucleotides encoding the polypeptides.
Summary of the Invention
The present invention relates to isolated polypeptides having
cellobiohydrolase
activity selected from the group consisting of:
(a) a polypeptide comprising an amino acid sequence having at least 99%
identity to the mature polypeptide of SEQ ID NO: 2;
(b) a polypeptide encoded by a polynucleotide comprising a nucleotide sequence
having at least 99% identity to the mature polypeptide coding sequence of SEQ
ID NO: 1;
and
(d) a polypeptide comprising the mature polypeptide of SEQ ID NO: 2, or a
fragment thereof having cellobiohydrolase activity.
The present invention also relates to isolated polynucleotides encoding the
polypeptides of the present invention; nucleic acid constructs, recombinant
expression
vectors, and recombinant host cells comprising the polynucleotides; and
methods of
producing the polypeptides.
The present invention also relates to methods for degrading or converting a
cellulosic
material, comprising: treating the cellulosic material with an enzyme
composition in the
presence of a polypeptide of the present invention.
The present invention also relates to methods for producing a fermentation
product,
comprising: (a) saccharifying a cellulosic material with an enzyme composition
in the
presence of a polypeptide of the present invention; (b) fermenting the
saccharified cellulosic
material with one or more fermenting microorganisms to produce the
fermentation product;
and (c) recovering the fermentation product from the fermentation
The present invention also relates to methods of fermenting a cellulosic
material,
comprising: fermenting the cellulosic material with one or more fermenting
microorganisms,
wherein the cellulosic material is saccharified with an enzyme composition in
the presence of
a polypeptide of the present invention.
The present invention also relates to a polynucleotide encoding a signal
peptide
comprising or consisting of amino acids 1 to 18 of SEQ ID NO: 2, which is
operably linked to
a gene encoding a protein; nucleic acid constructs, expression vectors, and
recombinant
host cells comprising the polynucleotides; and methods of producing a protein.
Brief Description of the Figures
Figures 1A and 1 B show the cDNA sequence and the deduced amino acid sequence
of an Aspergillus aculeatus strain NN000525 (IAM 2445) GH6 cellobiohydrolase
gene (SEQ
ID NOs: 1 and 2, respectively).
-2-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
Figure 2 shows the results of a 20% replacement (by protein) of a Trichoderma
reesei cellulolytic protein preparation (loaded at 2 mg per g of cellulose)
with A. aculeatus
cellobiohydrolase in the hydrolysis of pretreated corn stover.
Figure 3 shows a restriction map of pXYG1051-P6XY.
Figure 4 shows a restriction map of pCR2.1-P6XY.
Definitions
Cellobiohydrolase: The term "cellobiohydrolase" means a 1,4-beta-D-glucan
cellobiohydrolase (E.C. 3.2.1.91), which catalyzes the hydrolysis of 1,4-beta-
D-glucosidic
linkages in cellulose, cellooligosaccharides, or any beta-1,4-linked glucose
containing
polymer, releasing cellobiose from the reducing or non-reducing ends of the
chain (Teeri,
1997, Crystalline cellulose degradation: New insight into the function of
cellobiohydrolases,
Trends in Biotechnology 15: 160-167; Teeri et al., 1998, Trichoderma reesei
cellobiohydrolases: why so efficient on crystalline cellulose?, Biochem. Soc.
Trans. 26: 173-
178). For purposes of the present invention, cellobiohydrolase activity is
determined
according to the procedures described by Lever et al., 1972, Anal. Biochem.
47: 273-279;
van Tilbeurgh et al., 1982, FEBS Letters, 149: 152-156; van Tilbeurgh and
Claeyssens,
1985, FEBS Letters, 187: 283-288; and Tomme et al., 1988, Eur. J. Biochem.
170: 575-581;
and van Tilbeurgh et al., 1985, Eur. J. Biochem. 148: 329-334. The Lever et
al. method can
be employed to assess hydrolysis of cellulose in corn stover, while the
methods of van
Tilbeurgh et al. and Tomme et al. can be used to determine cellobiohydrolase I
activity on 4-
methylumbelliferyl-13-D-lactopyranoside.
Cellulolytic enzyme or cellulase: The term "cellulolytic enzyme" or
"cellulase"
means one or more (several) enzymes that hydrolyze a cellulosic material. Such
enzymes
include endoglucanase(s), cellobiohydrolase(s), beta-glucosidase(s), or
combinations
thereof. The two basic approaches for measuring cellulolytic activity include:
(1) measuring
the total cellulolytic activity, and (2) measuring the individual cellulolytic
activities
(endoglucanases, cellobiohydrolases, and beta-glucosidases) as reviewed in
Zhang et al.,
Outlook for cellulase improvement: Screening and selection strategies, 2006,
Biotechnology
Advances 24: 452-481. Total cellulolytic activity is usually measured using
insoluble
substrates, including Whatman NQ1 filter paper, microcrystalline cellulose,
bacterial cellulose,
algal cellulose, cotton, pretreated lignocellulose, etc. The most common total
cellulolytic
activity assay is the filter paper assay using Whatman NQ1 filter paper as the
substrate. The
assay was established by the International Union of Pure and Applied Chemistry
(IUPAC)
(Ghose, 1987, Measurement of cellulase activities, Pure Appl. Chem. 59: 257-
68).
For purposes of the present invention, cellulolytic enzyme activity is
determined by
measuring the increase in hydrolysis of a cellulosic material by cellulolytic
enzyme(s) under
-3-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
the following conditions: 1-20 mg of cellulolytic enzyme protein/g of
cellulose in PCS for 3-7
days at 50 C compared to a control hydrolysis without addition of cellulolytic
enzyme protein.
Typical conditions are 1 ml reactions, washed or unwashed PCS, 5% insoluble
solids, 50
mM sodium acetate pH 5, 1 mM MnSO4, 50 C, 72 hours, sugar analysis by AMINEX
HPX-
87H column (Bio-Rad Laboratories, Inc., Hercules, CA, USA).
Endoglucanase: The term "endoglucanase" means an endo-1,4-(1,3;1,4)-beta-D-
glucan 4-glucanohydrolase (E.C. 3.2.1.4), which catalyzes endohydrolysis of
1,4-beta-D-
glycosidic linkages in cellulose, cellulose derivatives (such as carboxymethyl
cellulose and
hydroxyethyl cellulose), lichenin, beta-1,4 bonds in mixed beta-1,3 glucans
such as cereal
beta-D-glucans or xyloglucans, and other plant material containing cellulosic
components.
Endoglucanase activity can be determined by measuring reduction in substrate
viscosity or
increase in reducing ends determined by a reducing sugar assay (Zhang et al.,
2006,
Biotechnology Advances 24: 452-481). For purposes of the present invention,
endoglucanase activity is determined using carboxymethyl cellulose (CMC) as
substrate
according to the procedure of Ghose, 1987, Pure and Appl. Chem. 59: 257-268,
at pH 5,
40 C.
Beta-glucosidase: The term "beta-glucosidase" means a beta-D-glucoside
glucohydrolase (E.C. 3.2.1.21), which catalyzes the hydrolysis of terminal non-
reducing
beta-D-glucose residues with the release of beta-D-glucose. For purposes of
the present
invention, beta-glucosidase activity is determined according to the basic
procedure
described by Venturi et al., 2002, Extracellular beta-D-glucosidase from
Chaetomium
thermophilum var. coprophilum: production, purification and some biochemical
properties, J.
Basic Microbiol. 42: 55-66. One unit of beta-glucosidase is defined as 1.0
pmole of p-
nitrophenolate anion produced per minute at 25 C, pH 4.8 from 1 mM p-
nitrophenyl-beta-D-
glucopyranoside as substrate in 50 mM sodium citrate containing 0.01% TWEEN
20.
Polypeptide having cellulolytic enhancing activity: The term "polypeptide
having
cellulolytic enhancing activity" means a GH61 polypeptide that enhances the
hydrolysis of a
cellulosic material by enzyme having cellulolytic activity. For purposes of
the present
invention, cellulolytic enhancing activity is determined by measuring the
increase in reducing
sugars or the increase of the total of cellobiose and glucose from the
hydrolysis of a
cellulosic material by cellulolytic enzyme under the following conditions: 1-
50 mg of total
protein/g of cellulose in PCS, wherein total protein is comprised of 50-99.5%
w/w cellulolytic
enzyme protein and 0.5-50% w/w protein of a GH61 polypeptide having
cellulolytic
enhancing activity for 1-7 days at 50 C compared to a control hydrolysis with
equal total
protein loading without cellulolytic enhancing activity (1-50 mg of
cellulolytic protein/g of
cellulose in PCS). In a preferred aspect, a mixture of CELLUCLAST 1.5L
(Novozymes A/S,
Bagsvaerd, Denmark) in the presence of 2-3% of total protein weight
Aspergillus oryzae
-4-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
beta-glucosidase (recombinantly produced in Aspergillus oryzae according to WO
02/095014) or 2-3% of total protein weight Aspergillus fumigatus beta-
glucosidase
(recombinantly produced in Aspergillus oryzae as described in WO 2002/095014)
of
cellulase protein loading is used as the source of the cellulolytic activity.
The GH61 polypeptides having cellulolytic enhancing activity enhance the
hydrolysis
of a cellulosic material catalyzed by enzyme having cellulolytic activity by
reducing the
amount of cellulolytic enzyme required to reach the same degree of hydrolysis
preferably at
least 1.01-fold, more preferably at least 1.05-fold, more preferably at least
1.10-fold, more
preferably at least 1.25-fold, more preferably at least 1.5-fold, more
preferably at least 2-fold,
more preferably at least 3-fold, more preferably at least 4-fold, more
preferably at least 5-
fold, even more preferably at least 10-fold, and most preferably at least 20-
fold.
Family 61 glycoside hydrolase: The term "Family 61 glycoside hydrolase" or
"Family GH61" or "GH61" means a polypeptide falling into the glycoside
hydrolase Family 61
according to Henrissat B., 1991, A classification of glycosyl hydrolases based
on amino-acid
sequence similarities, Biochem. J. 280: 309-316, and Henrissat B., and Bairoch
A., 1996,
Updating the sequence-based classification of glycosyl hydrolases, Biochem. J.
316: 695-
696.
Hemicellulolytic enzyme or hemicellulase: The term "hemicellulolytic enzyme"
or
"hemicellulase" means one or more (several) enzymes that hydrolyze a
hemicellulosic
material. See, for example, Shallom, D. and Shoham, Y. Microbial
hemicellulases. Current
Opinion In Microbiology, 2003, 6(3): 219-228). Hemicellulases are key
components in the
degradation of plant biomass. Examples of hemicellulases include, but are not
limited to, an
acetylmannan esterase, an acetyxylan esterase, an arabinanase, an
arabinofuranosidase, a
coumaric acid esterase, a feruloyl esterase, a galactosidase, a glucuronidase,
a glucuronoyl
esterase, a mannanase, a mannosidase, a xylanase, and a xylosidase. The
substrates of
these enzymes, the hemicelluloses, are a heterogeneous group of branched and
linear
polysaccharides that are bound via hydrogen bonds to the cellulose
microfibrils in the plant
cell wall, crosslinking them into a robust network. Hemicelluloses are also
covalently
attached to lignin, forming together with cellulose a highly complex
structure. The variable
structure and organization of hemicelluloses require the concerted action of
many enzymes
for its complete degradation. The catalytic modules of hemicellulases are
either glycoside
hydrolases (GHs) that hydrolyze glycosidic bonds, or carbohydrate esterases
(CEs), which
hydrolyze ester linkages of acetate or ferulic acid side groups. These
catalytic modules,
based on homology of their primary sequence, can be assigned into GH and CE
families
marked by numbers. Some families, with overall similar fold, can be further
grouped into
clans, marked alphabetically (e.g., GH-A). A most informative and updated
classification of
these and other carbohydrate active enzymes is available on the Carbohydrate-
Active
-5-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
Enzymes (CAZy) database. Hemicellulolytic enzyme activities can be measured
according to
Ghose and Bisaria, 1987, Pure & Appl. Chem. 59: 1739-1752.
Xylan degrading activity or xylanolytic activity: The term "xylan degrading
activity" or "xylanolytic activity" means a biological activity that
hydrolyzes xylan-containing
material. The two basic approaches for measuring xylanolytic activity include:
(1) measuring
the total xylanolytic activity, and (2) measuring the individual xylanolytic
activities (e.g.,
endoxylanases, beta-xylosidases, arabinofuranosidases, alpha-glucuronidases,
acetylxylan
esterases, feruloyl esterases, and alpha-glucuronyl esterases). Recent
progress in assays of
xylanolytic enzymes is summarized in several publications including Biely and
Puchard,
Recent progress in the assays of xylanolytic enzymes, 2006, Journal of the
Science of Food
and Agriculture 86(11): 1636-1647; Spanikova and Biely, 2006, Glucuronoyl
esterase -
Novel carbohydrate esterase produced by Schizophyllum commune, FEBS Letters
580(19):
4597-4601; Herrmann, Vrsanska, Jurickova, Hirsch, Biely, and Kubicek, 1997,
The beta-D-
xylosidase of Trichoderma reesei is a multifunctional beta-D-xylan
xylohydrolase,
Biochemical Journal 321: 375-381.
Total xylan degrading activity can be measured by determining the reducing
sugars
formed from various types of xylan, including, for example, oat spelt,
beechwood, and
larchwood xylans, or by photometric determination of dyed xylan fragments
released from
various covalently dyed xylans. The most common total xylanolytic activity
assay is based on
production of reducing sugars from polymeric 4-0-methyl glucuronoxylan as
described in
Bailey, Biely, Poutanen, 1992, Interlaboratory testing of methods for assay of
xylanase
activity, Journal of Biotechnology 23(3): 257-270. Xylanase activity can also
be determined
with 0.2% AZCL-arabinoxylan as substrate in 0.01% TRITON X-100 and 200 mM
sodium
phosphate buffer pH 6 at 37 C. One unit of xylanase activity is defined as 1.0
.tmole of
azurine produced per minute at 37 C, pH 6 from 0.2% AZCL-arabinoxylan as
substrate in
200 mM sodium phosphate pH 6 buffer.
For purposes of the present invention, xylan degrading activity is determined
by
measuring the increase in hydrolysis of birchwood xylan (Sigma Chemical Co.,
Inc., St.
Louis, MO, USA) by xylan-degrading enzyme(s) under the following typical
conditions: 1 ml
reactions, 5 mg/ml substrate (total solids), 5 mg of xylanolytic protein/g of
substrate, 50 mM
sodium acetate pH 5, 50 C, 24 hours, sugar analysis using p-hydroxybenzoic
acid hydrazide
(PHBAH) assay as described by Lever, 1972, A new reaction for colorimetric
determination
of carbohydrates, Anal. Biochem 47: 273-279.
Xylanase: The term "xylanase" means a 1,4-beta-D-xylan-xylohydrolase (E.C.
3.2.1.8) that catalyzes the endohydrolysis of 1,4-beta-D-xylosidic linkages in
xylans. For
purposes of the present invention, xylanase activity is determined with 0.2%
AZCL-
arabinoxylan as substrate in 0.01% TRITON X-100 and 200 mM sodium phosphate
buffer
-6-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
pH 6 at 37 C. One unit of xylanase activity is defined as 1.0 .tmole of
azurine produced per
minute at 37 C, pH 6 from 0.2% AZCL-arabinoxylan as substrate in 200 mM sodium
phosphate pH 6 buffer.
Beta-xylosidase: The term "beta-xylosidase" means a beta-D-xyloside
xylohydrolase (E.C. 3.2.1.37) that catalyzes the exo-hydrolysis of short beta-
(4) -
xylooligosaccharides, to remove successive D-xylose residues from the non-
reducing
termini. For purposes of the present invention, one unit of beta-xylosidase is
defined as 1.0
pmole of p-nitrophenolate anion produced per minute at 40 C, pH 5 from 1 mM p-
nitrophenyl-beta-D-xyloside as substrate in 100 mM sodium citrate containing
0.01%
TWEENO 20.
Acetylxylan esterase: The term "acetylxylan esterase" means a carboxylesterase
(EC 3.1.1.72) that catalyzes the hydrolysis of acetyl groups from polymeric
xylan, acetylated
xylose, acetylated glucose, alpha-napthyl acetate, and p-nitrophenyl acetate.
For purposes
of the present invention, acetylxylan esterase activity is determined using
0.5 mM p-
nitrophenylacetate as substrate in 50 mM sodium acetate pH 5.0 containing
0.01%
TWEENTM 20. One unit of acetylxylan esterase is defined as the amount of
enzyme capable
of releasing 1 pmole of p-nitrophenolate anion per minute at pH 5, 25 C.
Feruloyl esterase: The term "feruloyl esterase" means a 4-hydroxy-3-
methoxycinnamoyl-sugar hydrolase (EC 3.1.1.73) that catalyzes the hydrolysis
of the 4-
hydroxy-3-methoxycinnamoyl (feruloyl) group from an esterified sugar, which is
usually
arabinose in "natural" substrates, to produce ferulate (4-hydroxy-3-
methoxycinnamate).
Feruloyl esterase is also known as ferulic acid esterase, hydroxycinnamoyl
esterase, FAE-
III, cinnamoyl ester hydrolase, FAEA, cinnAE, FAE-I, or FAE-II. For purposes
of the present
invention, feruloyl esterase activity is determined using 0.5 mM p-
nitrophenylferulate as
substrate in 50 mM sodium acetate pH 5Ø One unit of feruloyl esterase equals
the amount
of enzyme capable of releasing 1 pmole of p-nitrophenolate anion per minute at
pH 5, 25 C.
Alpha-glucuronidase: The term "alpha-glucuronidase" means an alpha-D-
glucosiduronate glucuronohydrolase (EC 3.2.1.139) that catalyzes the
hydrolysis of an
alpha-D-glucuronoside to D-glucuronate and an alcohol. For purposes of the
present
invention, alpha-glucuronidase activity is determined according to de Vries,
1998, J.
Bacteriol. 180: 243-249. One unit of alpha-glucuronidase equals the amount of
enzyme
capable of releasing 1 pmole of glucuronic or 4-0-methylglucuronic acid per
minute at pH 5,
C.
Alpha-L-arabinofuranosidase: The term "alpha-L-arabinofuranosidase" means an
35 alpha-L-arabinofuranoside arabinofuranohydrolase (EC 3.2.1.55) that
catalyzes the
hydrolysis of terminal non-reducing alpha-L-arabinofuranoside residues in
alpha-L-
arabinosides. The enzyme acts on alpha-L-arabinofuranosides, alpha-L-arabinans
-7-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
containing (1,3)- and/or (1,5)-linkages, arabinoxylans, and arabinogalactans.
Alpha-L-
arabinofuranosidase is also known as arabinosidase, alpha-arabinosidase, alpha-
L-
arabinosidase, alpha-arabinofuranosidase, polysaccharide alpha-L-
arabinofuranosidase,
alpha-L-arabinofuranoside hydrolase, L-arabinosidase, or alpha-L-arabinanase.
For
purposes of the present invention, alpha-L-arabinofuranosidase activity is
determined using
5 mg of medium viscosity wheat arabinoxylan (Megazyme International Ireland,
Ltd., Bray,
Co. Wicklow, Ireland) per ml of 100 mM sodium acetate pH 5 in a total volume
of 200 pl for
30 minutes at 40 C followed by arabinose analysis by AMINEX HPX-87H column
chromatography (Bio-Rad Laboratories, Inc., Hercules, CA, USA).
Cellulosic material: The term "cellulosic material" means any material
containing
cellulose. The predominant polysaccharide in the primary cell wall of biomass
is cellulose,
the second most abundant is hemicellulose, and the third is pectin. The
secondary cell wall,
produced after the cell has stopped growing, also contains polysaccharides and
is
strengthened by polymeric lignin covalently cross-linked to hemicellulose.
Cellulose is a
homopolymer of anhydrocellobiose and thus a linear beta-(1-4)-D-glucan, while
hemicelluloses include a variety of compounds, such as xylans, xyloglucans,
arabinoxylans,
and mannans in complex branched structures with a spectrum of substituents.
Although
generally polymorphous, cellulose is found in plant tissue primarily as an
insoluble crystalline
matrix of parallel glucan chains. Hemicelluloses usually hydrogen bond to
cellulose, as well
as to other hemicelluloses, which help stabilize the cell wall matrix.
Cellulose is generally found, for example, in the stems, leaves, hulls, husks,
and
cobs of plants or leaves, branches, and wood of trees. The cellulosic material
can be, but is
not limited to, herbaceous material, agricultural residue, forestry residue,
municipal solid
waste, waste paper, and pulp and paper mill residue (see, for example,
Wiselogel et al.,
1995, in Handbook on Bioethanol (Charles E. Wyman, editor), pp.105-118, Taylor
& Francis,
Washington D.C.; Wyman, 1994, Bioresource Technology 50: 3-16; Lynd, 1990,
Applied
Biochemistry and Biotechnology 24/25: 695-719; Mosier et al., 1999, Recent
Progress in
Bioconversion of Lignocellulosics, in Advances in Biochemical
Engineering/Biotechnology, T.
Scheper, managing editor, Volume 65, pp.23-40, Springer-Verlag, New York). It
is
understood herein that the cellulose may be in the form of lignocellulose, a
plant cell wall
material containing lignin, cellulose, and hemicellulose in a mixed matrix. In
a preferred
aspect, the cellulosic material is lignocellulose, which comprises cellulose,
hemicellulose,
and lignin.
In one aspect, the cellulosic material is herbaceous material. In another
aspect, the
cellulosic material is agricultural residue. In another aspect, the cellulosic
material is forestry
residue. In another aspect, the cellulosic material is municipal solid waste.
In another aspect,
the cellulosic material is waste paper. In another aspect, the cellulosic
material is pulp and
-8-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
paper mill residue.
In another aspect, the cellulosic material is corn stover. In another aspect,
the
cellulosic material is corn fiber. In another aspect, the cellulosic material
is corn cob. In
another aspect, the cellulosic material is orange peel. In another aspect, the
cellulosic
material is rice straw. In another aspect, the cellulosic material is wheat
straw. In another
aspect, the cellulosic material is switch grass. In another aspect, the
cellulosic material is
miscanthus. In another aspect, the cellulosic material is bagasse.
In another aspect, the cellulosic material is microcrystalline cellulose. In
another
aspect, the cellulosic material is bacterial cellulose. In another aspect, the
cellulosic material
is algal cellulose. In another aspect, the cellulosic material is cotton
linter. In another aspect,
the cellulosic material is amorphous phosphoric-acid treated cellulose. In
another aspect, the
cellulosic material is filter paper.
The cellulosic material may be used as is or may be subjected to pretreatment,
using
conventional methods known in the art, as described herein. In a preferred
aspect, the
cellulosic material is pretreated.
Pretreated corn stover: The term "PCS" or "Pretreated Corn Stover" means a
cellulosic material derived from corn stover by treatment with heat and dilute
sulfuric acid.
Xylan-containing material: The term "xylan-containing material" means any
material comprising a plant cell wall polysaccharide containing a backbone of
beta-(1-4)-
linked xylose residues. Xylans of terrestrial plants are heteropolymers
possessing a beta-
(1-4)-D-xylopyra nose backbone, which is branched by short carbohydrate
chains. They
comprise D-glucuronic acid or its 4-0-methyl ether, L-arabinose, and/or
various
oligosaccharides, composed of D-xylose, L-arabinose, D- or L-galactose, and D-
glucose.
Xylan-type polysaccharides can be divided into homoxylans and heteroxylans,
which include
glucuronoxylans, (arabino)glucuronoxylans, (glucurono)arabinoxylans,
arabinoxylans, and
complex heteroxylans. See, for example, Ebringerova et al., 2005, Adv. Polym.
Sci. 186: 1-
67.
In the methods of the present invention, any material containing xylan may be
used.
In a preferred aspect, the xylan-containing material is lignocellulose.
Isolated or Purified: The term "isolated" or "purified" means a polypeptide or
polynucleotide that is removed from at least one component with which it is
naturally
associated. For example, a polypeptide may be at least 1% pure, e.g., at least
5% pure, at
least 10% pure, at least 20% pure, at least 40% pure, at least 60% pure, at
least 80% pure,
at least 90% pure, or at least 95% pure, as determined by SDS-PAGE, and a
polynucleotide
may be at least 1% pure, e.g., at least 5% pure, at least 10% pure, at least
20% pure, at
least 40% pure, at least 60% pure, at least 80% pure, at least 90% pure, or at
least 95%
pure, as determined by agarose electrophoresis.
-9-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
Mature polypeptide: The term "mature polypeptide" means a polypeptide in its
final
form following translation and any post-translational modifications, such as N-
terminal
processing, C-terminal truncation, glycosylation, phosphorylation, etc. In one
aspect, the
mature polypeptide is amino acids 19 to 469 of SEQ ID NO: 2 based on the
SignalP program
(Nielsen et al., 1997, Protein Engineering 10: 1-6) that predicts amino acids
1 to 18 of SEQ
ID NO: 2 are a signal peptide. It is known in the art that a host cell may
produce a mixture of
two of more different mature polypeptides (i.e., with a different C-terminal
and/or N-terminal
amino acid) expressed by the same polynucleotide.
Mature polypeptide coding sequence: The term "mature polypeptide coding
sequence" means a polynucleotide that encodes a mature polypeptide having
cellobiohydrolase activity. In one aspect, the mature polypeptide coding
sequence is
nucleotides 55 to 1407 of SEQ ID NO: 1 based on the SignalP program (Nielsen
et al., 1997,
supra) that predicts nucleotides 1 to 54 of SEQ ID NO: 1 encode a signal
peptide. In another
aspect, the mature polypeptide coding sequence is the genomic DNA sequence of
nucleotides 55 to 1407 of SEQ ID NO: 1.]
Sequence Identity: The relatedness between two amino acid sequences or between
two nucleotide sequences is described by the parameter "sequence identity".
For purposes of the present invention, the degree of sequence identity between
two
amino acid sequences is determined using the Needleman-Wunsch algorithm
(Needleman
and Wunsch, 1970, J. Mol. Biol. 48: 443-453) as implemented in the Needle
program of the
EMBOSS package (EMBOSS: The European Molecular Biology Open Software Suite,
Rice
et al., 2000, Trends Genet. 16: 276-277), preferably version 3Ø0 or later.
The optional
parameters used are gap open penalty of 10, gap extension penalty of 0.5, and
the
EBLOSUM62 (EMBOSS version of BLOSUM62) substitution matrix. The output of
Needle
labeled "longest identity" (obtained using the -nobrief option) is used as the
percent identity
and is calculated as follows:
(Identical Residues x 1 00)/(Length of Alignment - Total Number of Gaps in
Alignment)
For purposes of the present invention, the degree of sequence identity between
two
deoxyribonucleotide sequences is determined using the Needleman-Wunsch
algorithm
(Needleman and Wunsch, 1970, supra) as implemented in the Needle program of
the
EMBOSS package (EMBOSS: The European Molecular Biology Open Software Suite,
Rice
et al., 2000, supra), preferably version 3Ø0 or later. The optional
parameters used are gap
open penalty of 10, gap extension penalty of 0.5, and the EDNAFULL (EMBOSS
version of
NCBI NUC4.4) substitution matrix. The output of Needle labeled "longest
identity" (obtained
using the -nobrief option) is used as the percent identity and is calculated
as follows:
(Identical Deoxyribonucleotides x 100)/(Length of Alignment - Total Number of
Gaps in
Alignment)
-10-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
Fragment: The term "fragment" means a polypeptide having one or more (several)
amino acids deleted from the amino and/or carboxyl terminus of a mature
polypeptide;
wherein the fragment has cellobiohydrolase activity. In one aspect, a fragment
contains at
least 390 amino acid residues, e.g., at least 410 amino acid residues or at
least 430 amino
acid residues.
Subsequence: The term "subsequence" means a polynucleotide having one or more
(several) nucleotides deleted from the 5' and/or 3' end of a mature
polypeptide coding
sequence; wherein the subsequence encodes a fragment having cellobiohydrolase
activity.
In one aspect, a subsequence contains at least 1170 nucleotides, e.g., at
least 1230
nucleotides or at least 1290 nucleotides.
Allelic variant: The term "allelic variant" means any of two or more
alternative forms
of a gene occupying the same chromosomal locus. Allelic variation arises
naturally through
mutation, and may result in polymorphism within populations. Gene mutations
can be silent
(no change in the encoded polypeptide) or may encode polypeptides having
altered amino
acid sequences. An allelic variant of a polypeptide is a polypeptide encoded
by an allelic
variant of a gene.
Coding sequence: The term "coding sequence" means a polynucleotide, which
directly specifies the amino acid sequence of a polypeptide. The boundaries of
the coding
sequence are generally determined by an open reading frame, which usually
begins with the
ATG start codon or alternative start codons such as GTG and TTG and ends with
a stop
codon such as TAA, TAG, and TGA. The coding sequence may be a DNA, cDNA,
synthetic,
or recombinant polynucleotide.
cDNA: The term "cDNA" means a DNA molecule that can be prepared by reverse
transcription from a mature, spliced, mRNA molecule obtained from a eukaryotic
cell. cDNA
lacks intron sequences that may be present in the corresponding genomic DNA.
The initial,
primary RNA transcript is a precursor to mRNA that is processed through a
series of steps,
including splicing, before appearing as mature spliced mRNA.
Nucleic acid construct: The term "nucleic acid construct" means a nucleic acid
molecule, either single- or double-stranded, which is isolated from a
naturally occurring gene
or is modified to contain segments of nucleic acids in a manner that would not
otherwise
exist in nature or which is synthetic. The term nucleic acid construct is
synonymous with the
term "expression cassette" when the nucleic acid construct contains the
control sequences
required for expression of a coding sequence of the present invention.
Control sequences: The term "control sequences" means all components
necessary for the expression of a polynucleotide encoding a polypeptide of the
present
invention. Each control sequence may be native or foreign to the
polynucleotide encoding
the polypeptide or native or foreign to each other. Such control sequences
include, but are
-11-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
not limited to, a leader, polyadenylation sequence, propeptide sequence,
promoter, signal
peptide sequence, and transcription terminator. At a minimum, the control
sequences
include a promoter, and transcriptional and translational stop signals. The
control sequences
may be provided with linkers for the purpose of introducing specific
restriction sites
facilitating ligation of the control sequences with the coding region of the
polynucleotide
encoding a polypeptide.
Operably linked: The term "operably linked" means a configuration in which a
control sequence is placed at an appropriate position relative to the coding
sequence of a
polynucleotide such that the control sequence directs the expression of the
coding
sequence.
Expression: The term "expression" includes any step involved in the production
of
the polypeptide including, but not limited to, transcription, post-
transcriptional modification,
translation, post-translational modification, and secretion.
Expression vector: The term "expression vector" means a linear or circular DNA
molecule that comprises a polynucleotide encoding a polypeptide and is
operably linked to
additional nucleotides that provide for its expression.
Host cell: The term "host cell" means any cell type that is susceptible to
transformation, transfection, transduction, and the like with a nucleic acid
construct or
expression vector comprising a polynucleotide of the present invention. The
term "host cell"
encompasses any progeny of a parent cell that is not identical to the parent
cell due to
mutations that occur during replication.
Variant: The term "variant" means a polypeptide having cellobiohydrolase
activity
comprising an alteration, i.e., a substitution, insertion, and/or deletion of
one or more
(several) amino acid residues at one or more (several) positions. A
substitution means a
replacement of an amino acid occupying a position with a different amino acid;
a deletion
means removal of an amino acid occupying a position; and an insertion means
adding one
or more (several) amino acids, e.g., 1-5 amino acids, adjacent to an amino
acid occupying a
position.
Detailed Description of the Invention
Polypeptides Having Cellobiohydrolase Activity
The present invention relates to isolated polypeptides having
cellobiohydrolase
activity selected from the group consisting of:
(a) a polypeptide comprising an amino acid sequence having at least 99%
identity to the mature polypeptide of SEQ ID NO: 2;
(b) a polypeptide encoded by a polynucleotide comprising a nucleotide sequence
having at least 99% identity to the mature polypeptide coding sequence of SEQ
ID NO: 1;
-12-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
and
(d) a polypeptide comprising the mature polypeptide of SEQ ID NO: 2, or a
fragment thereof having cellobiohydrolase activity.
The present invention relates to isolated polypeptides having a sequence
identity to
the mature polypeptide of SEQ ID NO: 2 of at least 99%, e.g., 100%, which have
cellobiohydrolase activity. In one aspect, the polypeptides differ by no more
than ten amino
acids, e.g., by five amino acids, by four amino acids, by three amino acids,
by two amino
acids, and by one amino acid from the mature polypeptide of SEQ ID NO: 2.
A polypeptide of the present invention preferably comprises or consists of the
amino
acid sequence of SEQ ID NO: 2 or an allelic variant thereof; or is a fragment
thereof having
cellobiohydrolase activity. In another aspect, the polypeptide comprises or
consists of the
mature polypeptide of SEQ ID NO: 2. In another preferred aspect, the
polypeptide comprises
or consists of amino acids 19 to 469 of SEQ ID NO: 2.
The present invention also relates to isolated polypeptides having
cellobiohydrolase
activity that are encoded by polynucleotides that hybridize under very high
stringency
conditions with (i) the mature polypeptide coding sequence of SEQ ID NO: 1,
(ii) the
genomic DNA sequence of the mature polypeptide coding sequence of SEQ ID NO:
1, or (iii)
the full-length complementary strand of (i) or (ii) (J. Sambrook, E.F.
Fritsch, and T. Maniatis,
1989, Molecular Cloning, A Laboratory Manual, 2d edition, Cold Spring Harbor,
New York).
The polynucleotide of SEQ ID NO: 1 or a subsequence thereof, as well as the
amino
acid sequence of SEQ ID NO: 2 or a fragment thereof, may be used to design
nucleic acid
probes to identify and clone DNA encoding polypeptides having
cellobiohydrolase activity
from strains of different genera or species according to methods well known in
the art. In
particular, such probes can be used for hybridization with the genomic DNA or
cDNA of the
genus or species of interest, following standard Southern blotting procedures,
in order to
identify and isolate the corresponding gene therein. Such probes can be
considerably
shorter than the entire sequence, but should be at least 14, e.g., at least
25, at least 35, or at
least 70 nucleotides in length. Preferably, the nucleic acid probe is at least
100 nucleotides
in length, e.g., at least 200 nucleotides, at least 300 nucleotides, at least
400 nucleotides, at
least 500 nucleotides, at least 600 nucleotides, at least 700 nucleotides, at
least 800
nucleotides, or at least 900 nucleotides in length. Both DNA and RNA probes
can be used.
The probes are typically labeled for detecting the corresponding gene (for
example, with 32P,
3H 35S, biotin, or avidin). Such probes are encompassed by the present
invention.
A genomic DNA or cDNA library prepared from such other strains may be screened
for DNA that hybridizes with the probes described above and encodes a
polypeptide having
cellobiohydrolase activity. Genomic or other DNA from such other strains may
be separated
by agarose or polyacrylamide gel electrophoresis, or other separation
techniques. DNA from
-13-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
the libraries or the separated DNA may be transferred to and immobilized on
nitrocellulose
or other suitable carrier material. In order to identify a clone or DNA that
is homologous with
SEQ ID NO: 1 or a subsequence thereof, the carrier material is preferably used
in a
Southern blot.
For purposes of the present invention, hybridization indicates that the
polynucleotide
hybridizes to a labeled nucleic acid probe corresponding to SEQ ID NO: 1; the
mature
polypeptide coding sequence of SEQ ID NO: 1; the genomic DNA sequence of the
mature
polypeptide coding sequence of SEQ ID NO: 1; its full-length complementary
strand; or a
subsequence thereof; under very low to very high stringency conditions.
Molecules to which
the nucleic acid probe hybridizes under these conditions can be detected
using, for example,
X-ray film.
In one aspect, the nucleic acid probe is the mature polypeptide coding
sequence of
SEQ ID NO: 1 or the genomic DNA sequence thereof. In another aspect, the
nucleic acid
probe is a polynucleotide that encodes the polypeptide of SEQ ID NO: 2 or the
mature
polypeptide thereof; or a fragment thereof. In another preferred aspect, the
nucleic acid
probe is SEQ ID NO: 1 or the genomic DNA sequence thereof. In another aspect,
the nucleic
acid probe is the polynucleotide contained in plasmid pCR2.1-P6XY which is
contained in E.
coli DSM 22994, wherein the polynucleotide encodes a polypeptide having
cellobiohydrolase
activity. In another aspect, the nucleic acid probe is the mature polypeptide
coding region
contained in plasmid pCR2.1-P6XY which is contained in E. coli DSM 22994.
For long probes of at least 100 nucleotides in length, very low to very high
stringency
conditions are defined as prehybridization and hybridization at 42 C in 5X
SSPE, 0.3% SDS,
200 micrograms/ml sheared and denatured salmon sperm DNA, and either 25%
formamide
for very low and low stringencies, 35% formamide for medium and medium-high
stringencies, or 50% formamide for high and very high stringencies, following
standard
Southern blotting procedures for 12 to 24 hours optimally. The carrier
material is finally
washed three times each for 15 minutes using 2X SSC, 0.2% SDS at 45 C (very
low
stringency), at 50 C (low stringency), at 55 C (medium stringency), at 60 C
(medium-high
stringency), at 65 C (high stringency), and at 70 C (very high stringency).
For short probes of about 15 nucleotides to about 70 nucleotides in length,
stringency
conditions are defined as prehybridization and hybridization at about 5 C to
about 10 C
below the calculated T,õ using the calculation according to Bolton and
McCarthy (1962, Proc.
Natl. Acad. Sci. USA 48:1390) in 0.9 M NaCl, 0.09 M Tris-HCI pH 7.6, 6 mM
EDTA, 0.5%
NP-40, 1X Denhardt's solution, 1 mM sodium pyrophosphate, 1 mM sodium
monobasic
phosphate, 0.1 mM ATP, and 0.2 mg of yeast RNA per ml following standard
Southern
blotting procedures for 12 to 24 hours optimally. The carrier material is
finally washed once
in 6X SCC plus 0.1% SDS for 15 minutes and twice each for 15 minutes using 6X
SSC at
-14-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
C to 10 C below the calculated T,,,.
The present invention also relates to isolated polypeptides having
cellobiohydrolase
activity encoded by polynucleotides having a sequence identity to the mature
polypeptide
coding sequence of SEQ ID NO: 1 or the genomic DNA sequence thereof of at
least 99%,
5 e.g., 100%.
The present invention also relates to variants comprising a substitution,
deletion,
and/or insertion of one or more (or several) amino acids of the mature
polypeptide of SEQ ID
NO: 2, or a homologous sequence thereof. Preferably, amino acid changes are of
a minor
nature, that is conservative amino acid substitutions or insertions that do
not significantly
affect the folding and/or activity of the protein; small deletions, typically
of one to about 30
amino acids; small amino- or carboxyl-terminal extensions, such as an amino-
terminal
methionine residue; a small linker peptide of up to about 20-25 residues; or a
small
extension that facilitates purification by changing net charge or another
function, such as a
poly-histidine tract, an antigenic epitope or a binding domain.
Examples of conservative substitutions are within the group of basic amino
acids
(arginine, lysine and histidine), acidic amino acids (glutamic acid and
aspartic acid), polar
amino acids (glutamine and asparagine), hydrophobic amino acids (leucine,
isoleucine and
valine), aromatic amino acids (phenylalanine, tryptophan and tyrosine), and
small amino
acids (glycine, alanine, serine, threonine and methionine). Amino acid
substitutions that do
not generally alter specific activity are known in the art and are described,
for example, by H.
Neurath and R.L. Hill, 1979, In, The Proteins, Academic Press, New York. The
most
commonly occurring exchanges are Ala/Ser, Val/Ile, Asp/Glu, Thr/Ser, Ala/Gly,
Ala/Thr,
Ser/Asn, Ala/Val, Ser/Gly, Tyr/Phe, Ala/Pro, Lys/Arg, Asp/Asn, Leu/Ile,
Leu/Val, Ala/Glu, and
Asp/Gly.
Alternatively, the amino acid changes are of such a nature that the physico-
chemical
properties of the polypeptides are altered. For example, amino acid changes
may improve
the thermal stability of the polypeptide, alter the substrate specificity,
change the pH
optimum, and the like.
Essential amino acids in a parent polypeptide can be identified according to
procedures known in the art, such as site-directed mutagenesis or alanine-
scanning
mutagenesis (Cunningham and Wells, 1989, Science 244: 1081-1085). In the
latter
technique, single alanine mutations are introduced at every residue in the
molecule, and the
resultant mutant molecules are tested for cellobiohydrolase activity to
identify amino acid
residues that are critical to the activity of the molecule. See also, Hilton
et al., 1996, J. Biol.
Chem. 271: 4699-4708. The active site of the enzyme or other biological
interaction can also
be determined by physical analysis of structure, as determined by such
techniques as
nuclear magnetic resonance, crystallography, electron diffraction, or
photoaffinity labeling, in
-15-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
conjunction with mutation of putative contact site amino acids. See, for
example, de Vos et
al., 1992, Science 255: 306-312; Smith et al., 1992, J. Mol. Biol. 224: 899-
904; Wlodaver et
al., 1992, FEBS Lett. 309: 59-64. The identities of essential amino acids can
also be inferred
from analysis of identities with polypeptides that are related to the parent
polypeptide.
Single or multiple amino acid substitutions, deletions, and/or insertions can
be made
and tested using known methods of mutagenesis, recombination, and/or
shuffling, followed
by a relevant screening procedure, such as those disclosed by Reidhaar-Olson
and Sauer,
1988, Science 241: 53-57; Bowie and Sauer, 1989, Proc. Natl. Acad. Sci. USA
86: 2152-
2156; WO 95/17413; or WO 95/22625. Other methods that can be used include
error-prone
PCR, phage display (e.g., Lowman et al., 1991, Biochemistry 30: 10832-10837;
U.S. Patent
No. 5,223,409; WO 92/06204), and region-directed mutagenesis (Derbyshire et
al., 1986,
Gene 46: 145; Ner et al., 1988, DNA 7: 127).
Mutagenesis/shuffling methods can be combined with high-throughput, automated
screening methods to detect activity of cloned, mutagenized polypeptides
expressed by host
cells (Ness et al., 1999, Nature Biotechnology 17: 893-896). Mutagenized DNA
molecules
that encode active polypeptides can be recovered from the host cells and
rapidly sequenced
using standard methods in the art. These methods allow the rapid determination
of the
importance of individual amino acid residues in a polypeptide.
The total number of amino acid substitutions, deletions and/or insertions of
the
mature polypeptide of SEQ ID NO: 2 is not more than 10, e.g., 1, 2, 3, 4, 5,
6, 7, 8 or 9.
The polypeptide may be hybrid polypeptide in which a portion of one
polypeptide is
fused at the N-terminus or the C-terminus of a portion of another polypeptide.
The polypeptide may be a fused polypeptide or cleavable fusion polypeptide in
which
another polypeptide is fused at the N-terminus or the C-terminus of the
polypeptide of the
present invention. A fused polypeptide is produced by fusing a polynucleotide
encoding
another polypeptide to a polynucleotide of the present invention. Techniques
for producing
fusion polypeptides are known in the art, and include ligating the coding
sequences
encoding the polypeptides so that they are in frame and that expression of the
fused
polypeptide is under control of the same promoter(s) and terminator. Fusion
proteins may
also be constructed using intein technology in which fusions are created post-
translationally
(Cooper et al., 1993, EMBO J. 12: 2575-2583; Dawson et al., 1994, Science 266:
776-779).
A fusion polypeptide can further comprise a cleavage site between the two
polypeptides. Upon secretion of the fusion protein, the site is cleaved
releasing the two
polypeptides. Examples of cleavage sites include, but are not limited to, the
sites disclosed
in Martin et al., 2003, J. Ind. Microbiol. Biotechnol. 3: 568-576; Svetina et
al., 2000, J.
Biotechnol. 76: 245-251; Rasmussen-Wilson etal., 1997, Appl. Environ.
Microbiol. 63: 3488-
3493; Ward et al., 1995, Biotechnology 13: 498-503; and Contreras et al.,
1991,
-16-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
Biotechnology 9: 378-381; Eaton et al., 1986, Biochemistry 25: 505-512;
Collins-Racie et al.,
1995, Biotechnology 13: 982-987; Carter et al., 1989, Proteins: Structure,
Function, and
Genetics 6: 240-248; and Stevens, 2003, Drug Discovery World 4: 35-48.
Sources of Polypeptides Having Cellobiohydrolase Activity
A polypeptide having cellobiohydrolase activity of the present invention may
be
obtained from microorganisms of any genus. For purposes of the present
invention, the term
"obtained from" as used herein in connection with a given source shall mean
that the
polypeptide encoded by a polynucleotide is produced by the source or by a
strain in which
the polynucleotide from the source has been inserted. In one aspect, the
polypeptide
obtained from a given source is secreted extracellularly.
The polypeptide may be a bacterial polypeptide. For example, the polypeptide
may
be a gram-positive bacterial polypeptide such as a Bacillus, Clostridium,
Enterococcus,
Geobacillus, Lactobacillus, Lactococcus, Oceanobacillus, Staphylococcus,
Streptococcus, or
Streptomyces polypeptide having cellobiohydrolase activity, or a gram-negative
bacterial
polypeptide such as a Campylobacter, E. coli, Flavobacterium, Fusobacterium,
Helicobacter,
Ilyobacter, Neisseria, Pseudomonas, Salmonella, or Ureaplasma polypeptide.
In one aspect, the polypeptide is a Bacillus alkalophilus, Bacillus
amyloliquefaciens,
Bacillus brevis, Bacillus circulans, Bacillus clausii, Bacillus coagulans,
Bacillus firm us,
Bacillus lautus, Bacillus lentus, Bacillus licheniformis, Bacillus megaterium,
Bacillus pumilus,
Bacillus stearothermophilus, Bacillus subtilis, or Bacillus thuringiensis
polypeptide.
In another aspect, the polypeptide is a Streptococcus equisimilis,
Streptococcus
pyogenes, Streptococcus uberis, or Streptococcus equi subsp. Zooepidemicus
polypeptide.
In another aspect, the polypeptide is a Streptomyces achromogenes,
Streptomyces
avermitilis, Streptomyces coelicolor, Streptomyces griseus, or Streptomyces
lividans
polypeptide.
The polypeptide may also be a fungal polypeptide. For example, the polypeptide
may
be a yeast polypeptide such as a Candida, Kluyveromyces, Pichia,
Saccharomyces,
Schizosaccharomyces, or Yarrowia polypeptide; or a filamentous fungal
polypeptide such as
an Acremonium, Agaricus, Alternaria, Aspergillus, Aureobasidium,
Botryospaeria,
Ceriporiopsis, Chaetomidium, Chrysosporium, Claviceps, Cochliobolus,
Coprinopsis,
Coptotermes, Corynascus, Cryphonectria, Cryptococcus, Diplodia, Exidia,
Filibasidium,
Fusarium, Gibberella, Holomastigotoides, Humicola, Irpex, Lentinula,
Leptospaeria,
Magnaporthe, Melanocarpus, Meripilus, Mucor, Myceliophthora, Neocallimastix,
Neurospora,
Paecilomyces, Penicillium, Phanerochaete, Piromyces, Poitrasia,
Pseudoplectania,
Pseudotrichonympha, Rhizomucor, Schizophyllum, Scytalidium, Talaromyces,
Thermoascus, Thielavia, Tolypocladium, Trichoderma, Trichophaea, Verticillium,
Volvariella,
-17-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
or Xylaria polypeptide.
In another aspect, the polypeptide is a Saccharomyces carlsbergensis,
Saccharomyces cerevisiae, Saccharomyces diastaticus, Saccharomyces douglasii,
Saccharomyces kluyveri, Saccharomyces norbensis, or Saccharomyces oviformis
polypeptide.
In another aspect, the polypeptide is an Acremonium cellulolyticus,
Aspergillus
aculeatus, Aspergillus awamori, Aspergillus foetidus, Aspergillus fumigatus,
Aspergillus
japonicus, Aspergillus nidulans, Aspergillus niger, Aspergillus oryzae,
Chrysosporium inops,
Chrysosporium keratinophilum, Chrysosporium lucknowense, Chrysosporium
merdarium,
Chrysosporium pannicola, Chrysosporium queenslandicum, Chrysosporium tropicum,
Chrysosporium zonatum, Fusarium bactridioides, Fusarium cerealis, Fusarium
crookwellense, Fusarium culmorum, Fusarium graminearum, Fusarium graminum,
Fusarium
heterosporum, Fusarium negundi, Fusarium oxysporum, Fusarium reticulatum,
Fusarium
roseum, Fusarium sambucinum, Fusarium sarcochroum, Fusarium sporotrichioides,
Fusarium sulphureum, Fusarium torulosum, Fusarium trichothecioides, Fusarium
venenatum, Humicola grisea, Humicola insolens, Humicola lanuginosa, Irpex
lacteus, Mucor
miehei, Myceliophthora thermophila, Neurospora crassa, Penicillium
funiculosum,
Penicillium purpurogenum, Phanerochaete chrysosporium, Thielavia achromatica,
Thielavia
albomyces, Thielavia albopilosa, Thielavia australeinsis, Thielavia fimeti,
Thielavia
microspora, Thielavia ovispora, Thielavia peruviana, Thielavia setosa,
Thielavia
spededonium, Thielavia subthermophila, Thielavia terrestris, Trichoderma
harzianum,
Trichoderma koningii, Trichoderma longibrachiatum, Trichoderma reesei, or
Trichoderma
viride polypeptide.
In another aspect, the polypeptide is an Aspergillus aculeatus polypeptide
having
cellobiohydrolase activity. In another aspect, the polypeptide is an
Aspergillus aculeatus IAM
2445 polypeptide having cellobiohydrolase activity, e.g., the polypeptide
comprising the
mature polypeptide of SEQ ID NO: 2.
It will be understood that for the aforementioned species the invention
encompasses
both the perfect and imperfect states, and other taxonomic equivalents, e.g.,
anamorphs,
regardless of the species name by which they are known. Those skilled in the
art will readily
recognize the identity of appropriate equivalents.
Strains of these species are readily accessible to the public in a number of
culture
collections, such as the American Type Culture Collection (ATCC), Deutsche
Sammlung von
Mikroorganismen and Zellkulturen GmbH (DSMZ), Centraalbureau Voor
Schimmelcultures
(CBS), and Agricultural Research Service Patent Culture Collection, Northern
Regional
Research Center (NRRL).
The polypeptide may be identified and obtained from other sources including
-18-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
microorganisms isolated from nature (e.g., soil, composts, water, etc.) using
the above-
mentioned probes. Techniques for isolating microorganisms from natural
habitats are well
known in the art. The polynucleotide encoding the polypeptide may then be
obtained by
similarly screening a genomic DNA or cDNA library of another microorganism or
mixed DNA
sample. Once a polynucleotide encoding a polypeptide has been detected with
the probe(s),
the polynucleotide can be isolated or cloned by utilizing techniques that are
well known to
those of ordinary skill in the art (see, e.g., Sambrook et al., 1989, supra).
Polynucleotides
The present invention also relates to isolated polynucleotides encoding a
polypeptide
of the present invention.
The techniques used to isolate or clone a polynucleotide encoding a
polypeptide are
known in the art and include isolation from genomic DNA, preparation from
cDNA, or a
combination thereof. The cloning of the polynucleotides from such genomic DNA
can be
effected, e.g., by using the well known polymerase chain reaction (PCR) or
antibody
screening of expression libraries to detect cloned DNA fragments with shared
structural
features. See, e.g., Innis et al., 1990, PCR: A Guide to Methods and
Application, Academic
Press, New York. Other nucleic acid amplification procedures such as ligase
chain reaction
(LCR), ligation activated transcription (LAT) and polynucleotide-based
amplification (NASBA)
may be used. The polynucleotides may be cloned from a strain of Aspergillus,
or a related
organism and thus, for example, may be an allelic or species variant of the
polypeptide
encoding region of the polynucleotide.
The present invention also relates to isolated polynucleotides comprising or
consisting of polynucleotides having a degree of sequence identity to the
mature polypeptide
coding sequence of SEQ ID NO: 1 or the genomic DNA sequence thereof of at
least 99%,
e.g., 100%, which encode a polypeptide having cellobiohydrolase activity.
Modification of a polynucleotide encoding a polypeptide of the present
invention may
be necessary for the synthesis of polypeptides substantially similar to the
polypeptide. The
term "substantially similar" to the polypeptide refers to non-naturally
occurring forms of the
polypeptide. These polypeptides may differ in some engineered way from the
polypeptide
isolated from its native source, e.g., variants that differ in specific
activity, thermostability, pH
optimum, or the like. The variant may be constructed on the basis of the
polynucleotide
presented as the mature polypeptide coding sequence of SEQ ID NO: 1 or the
genomic DNA
sequence thereof, e.g., a subsequence thereof, and/or by introduction of
nucleotide
substitutions that do not result in a change in the amino acid sequence of the
polypeptide,
but which correspond to the codon usage of the host organism intended for
production of the
enzyme, or by introduction of nucleotide substitutions that may give rise to a
different amino
-19-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
acid sequence. For a general description of nucleotide substitution, see,
e.g., Ford et al.,
1991, Protein Expression and Purification 2: 95-107.
The present invention also relates to isolated polynucleotides encoding
polypeptides
of the present invention, which hybridize under very low stringency
conditions, low
stringency conditions, medium stringency conditions, medium-high stringency
conditions,
high stringency conditions, or very high stringency conditions with (i) the
mature polypeptide
coding sequence of SEQ ID NO: 1, (ii) the genomic DNA sequence of the mature
polypeptide coding sequence of SEQ ID NO: 1, or (iii) the full-length
complementary strand
of (i) or (ii); or allelic variants and subsequences thereof (Sambrook et al.,
1989, supra), as
defined herein.
In one aspect, the polynucleotide comprises or consists of SEQ ID NO: 1, the
mature
polypeptide coding sequence of SEQ ID NO: 1, or the sequence contained in
plasmid
pCR2.1-P6XY which is contained in E. coli DSM 22994, or a subsequence of SEQ
ID NO: 1
that encodes a fragment of SEQ ID NO: 2 having cellobiohydrolase activity,
such as the
polynucleotide of nucleotides 55 to 1407 of SEQ ID NO: 1.
Nucleic Acid Constructs
The present invention also relates to nucleic acid constructs comprising a
polynucleotide of the present invention operably linked to one or more
(several) control
sequences that direct the expression of the coding sequence in a suitable host
cell under
conditions compatible with the control sequences.
A polynucleotide may be manipulated in a variety of ways to provide for
expression of
the polypeptide. Manipulation of the polynucleotide prior to its insertion
into a vector may be
desirable or necessary depending on the expression vector. The techniques for
modifying
polynucleotides utilizing recombinant DNA methods are well known in the art.
The control sequence may be a promoter sequence, a polynucleotide that is
recognized by a host cell for expression of a polynucleotide encoding a
polypeptide of the
present invention. The promoter sequence contains transcriptional control
sequences that
mediate the expression of the polypeptide. The promoter may be any
polynucleotide that
shows transcriptional activity in the host cell of choice including mutant,
truncated, and
hybrid promoters, and may be obtained from genes encoding extracellular or
intracellular
polypeptides either homologous or heterologous to the host cell.
Examples of suitable promoters for directing the transcription of the nucleic
acid
constructs of the present invention in a bacterial host cell are the promoters
obtained from
the Bacillus amyloliquefaciens alpha-amylase gene (amyQ), Bacillus
licheniformis alpha-
amylase gene (amyL), Bacillus licheniformis penicillinase gene (penP),
Bacillus
stearothermophilus maltogenic amylase gene (amyM), Bacillus subtilis
levansucrase gene
-20-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
(sacB), Bacillus subtilis xylA and xy1B genes, E. coli lac operon,
Streptomyces coelicolor
agarase gene (dagA), and prokaryotic beta-lactamase gene (Villa-Kamaroff et
al., 1978,
Proc. Natl. Acad. Sci. USA 75: 3727-3731), as well as the tac promoter (DeBoer
et al., 1983,
Proc. Natl. Acad. Sci. USA 80: 21-25). Further promoters are described in
"Useful proteins
from recombinant bacteria" in Gilbert et al., 1980, Scientific American, 242:
74-94; and in
Sambrook et al., 1989, supra.
Examples of suitable promoters for directing the transcription of the nucleic
acid
constructs of the present invention in a filamentous fungal host cell are
promoters obtained
from the genes for Aspergillus nidulans acetamidase, Aspergillus niger neutral
alpha-
amylase, Aspergillus niger acid stable alpha-amylase, Aspergillus niger or
Aspergillus
awamori glucoamylase (glaA), Aspergillus oryzae TAKA amylase, Aspergillus
oryzae
alkaline protease, Aspergillus oryzae triose phosphate isomerase, Fusarium
oxysporum
trypsin-like protease (WO 96/00787), Fusarium venenatum amyloglucosidase (WO
00/56900), Fusarium venenatum Daria (WO 00/56900), Fusarium venenatum Quinn
(WO
00/56900), Rhizomucor miehei lipase, Rhizomucor miehei aspartic proteinase,
Trichoderma
reesei beta-glucosidase, Trichoderma reesei cellobiohydrolase I, Trichoderma
reesei
cellobiohydrolase II, Trichoderma reesei endoglucanase I, Trichoderma reesei
endoglucanase II, Trichoderma reesei endoglucanase III, Trichoderma reesei
endoglucanase IV, Trichoderma reesei endoglucanase V, Trichoderma reesei
xylanase I,
Trichoderma reesei xylanase II, Trichoderma reesei beta-xylosidase, as well as
the NA2-tpi
promoter (a modified promoter from a gene encoding a neutral alpha-amylase in
Aspergilli in
which the untranslated leader has been replaced by an untranslated leader from
a gene
encoding triose phosphate isomerase in Aspergilli; non-limiting examples
include modified
promoters from the gene encoding neutral alpha-amylase in Aspergillus niger in
which the
untranslated leader has been replaced by an untranslated leader from the gene
encoding
triose phosphate isomerase in Aspergillus nidulans or Aspergillus oryzae); and
mutant,
truncated, and hybrid promoters thereof.
In a yeast host, useful promoters are obtained from the genes for
Saccharomyces
cerevisiae enolase (ENO-1), Saccharomyces cerevisiae galactokinase (GAL1),
Saccharomyces cerevisiae alcohol dehydrogenase/glyceraldehyde-3-phosphate
dehydrogenase (ADH1, ADH2/GAP), Saccharomyces cerevisiae triose phosphate
isomerase (TPI), Saccharomyces cerevisiae metallothionein (CUP1), and
Saccharomyces
cerevisiae 3-phosphoglycerate kinase. Other useful promoters for yeast host
cells are
described by Romanos et al., 1992, Yeast 8: 423-488.
The control sequence may also be a suitable transcription terminator sequence,
which is recognized by a host cell to terminate transcription. The terminator
sequence is
operably linked to the 3'-terminus of the polynucleotide encoding the
polypeptide. Any
-21 -
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
terminator that is functional in the host cell of choice may be used in the
present invention.
Preferred terminators for filamentous fungal host cells are obtained from the
genes
for Aspergillus nidulans anthranilate synthase, Aspergillus niger
glucoamylase, Aspergillus
niger alpha-glucosidase, Aspergillus oryzae TAKA amylase, and Fusarium
oxysporum
trypsin-like protease.
Preferred terminators for yeast host cells are obtained from the genes for
Saccharomyces cerevisiae enolase, Saccharomyces cerevisiae cytochrome C
(CYC1), and
Saccharomyces cerevisiae glyceraldehyde-3-phosphate dehydrogenase. Other
useful
terminators for yeast host cells are described by Romanos et al., 1992, supra.
The control sequence may also be a suitable leader sequence, when transcribed
is a
nontranslated region of an mRNA that is important for translation by the host
cell. The leader
sequence is operably linked to the 5'-terminus of the polynucleotide encoding
the
polypeptide. Any leader sequence that is functional in the host cell of choice
may be used.
Preferred leaders for filamentous fungal host cells are obtained from the
genes for
Aspergillus oryzae TAKA amylase and Aspergillus nidulans triose phosphate
isomerase.
Suitable leaders for yeast host cells are obtained from the genes for
Saccharomyces
cerevisiae enolase (ENO-1), Saccharomyces cerevisiae 3-phosphoglycerate
kinase,
Saccharomyces cerevisiae alpha-factor, and Saccharomyces cerevisiae alcohol
dehydrogenase/glyceraldehyde-3-phosphate dehydrogenase (ADH2/GAP).
The control sequence may also be a polyadenylation sequence, a sequence
operably linked to the 3'-terminus of the polynucleotide and, when
transcribed, is recognized
by the host cell as a signal to add polyadenosine residues to transcribed
mRNA. Any
polyadenylation sequence that is functional in the host cell of choice may be
used.
Preferred polyadenylation sequences for filamentous fungal host cells are
obtained
from the genes for Aspergillus oryzae TAKA amylase, Aspergillus niger
glucoamylase,
Aspergillus nidulans anthranilate synthase, Fusarium oxysporum trypsin-like
protease, and
Aspergillus niger alpha-glucosidase.
Useful polyadenylation sequences for yeast host cells are described by Guo and
Sherman, 1995, Mol. Cellular Biol. 15: 5983-5990.
The control sequence may also be a signal peptide coding region that encodes a
signal peptide linked to the N-terminus of a polypeptide and directs the
polypeptide into the
cell's secretory pathway. The 5'-end of the coding sequence of the
polynucleotide may
inherently contain a signal peptide coding sequence naturally linked in
translation reading
frame with the segment of the coding sequence that encodes the polypeptide.
Alternatively,
the 5'-end of the coding sequence may contain a signal peptide coding sequence
that is
foreign to the coding sequence. The foreign signal peptide coding sequence may
be
required where the coding sequence does not naturally contain a signal peptide
coding
-22-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
sequence. Alternatively, the foreign signal peptide coding sequence may simply
replace the
natural signal peptide coding sequence in order to enhance secretion of the
polypeptide.
However, any signal peptide coding sequence that directs the expressed
polypeptide into
the secretory pathway of a host cell of choice may be used.
Effective signal peptide coding sequences for bacterial host cells are the
signal
peptide coding sequences obtained from the genes for Bacillus NCIB 11837
maltogenic
amylase, Bacillus licheniformis subtilisin, Bacillus licheniformis beta-
lactamase, Bacillus
stearothermophilus alpha-amylase, Bacillus stearothermophilus neutral
proteases (nprT,
nprS, nprM), and Bacillus subtilis prsA. Further signal peptides are described
by Simonen
and Palva, 1993, Microbiological Reviews 57: 109-137.
Effective signal peptide coding sequences for filamentous fungal host cells
are the
signal peptide coding sequences obtained from the genes for Aspergillus niger
neutral
amylase, Aspergillus niger glucoamylase, Aspergillus oryzae TAKA amylase,
Humicola
insolens cellulase, Humicola insolens endoglucanase V, Humicola lanuginosa
lipase, and
Rhizomucor miehei aspartic proteinase.
Useful signal peptides for yeast host cells are obtained from the genes for
Saccharomyces cerevisiae alpha-factor and Saccharomyces cerevisiae invertase.
Other
useful signal peptide coding sequences are described by Romanos et al., 1992,
supra.
The control sequence may also be a propeptide coding sequence that encodes a
propeptide positioned at the N-terminus of a polypeptide. The resultant
polypeptide is known
as a proenzyme or propolypeptide (or a zymogen in some cases). A
propolypeptide is
generally inactive and can be converted to an active polypeptide by catalytic
or autocatalytic
cleavage of the propeptide from the propolypeptide. The propeptide coding
sequence may
be obtained from the genes for Bacillus subtilis alkaline protease (aprE),
Bacillus subtilis
neutral protease (nprT), Myceliophthora thermophila laccase (WO 95/33836),
Rhizomucor
miehei aspartic proteinase, and Saccharomyces cerevisiae alpha-factor.
Where both signal peptide and propeptide sequences are present at the N-
terminus
of a polypeptide, the propeptide sequence is positioned next to the N-terminus
of a
polypeptide and the signal peptide sequence is positioned next to the N-
terminus of the
propeptide sequence.
It may also be desirable to add regulatory sequences that allow the regulation
of the
expression of the polypeptide relative to the growth of the host cell.
Examples of regulatory
systems are those that cause the expression of the gene to be turned on or off
in response
to a chemical or physical stimulus, including the presence of a regulatory
compound.
Regulatory systems in prokaryotic systems include the lac, tac, and trp
operator systems. In
yeast, the ADH2 system or GAL1 system may be used. In filamentous fungi, the
Aspergillus
niger glucoamylase promoter, Aspergillus oryzae TAKA alpha-amylase promoter,
and
-23-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
Aspergillus oryzae glucoamylase promoter may be used. Other examples of
regulatory
sequences are those that allow for gene amplification. In eukaryotic systems,
these
regulatory sequences include the dihydrofolate reductase gene that is
amplified in the
presence of methotrexate, and the metallothionein genes that are amplified
with heavy
metals. In these cases, the polynucleotide encoding the polypeptide would be
operably
linked with the regulatory sequence.
Expression Vectors
The present invention also relates to recombinant expression vectors
comprising a
polynucleotide of the present invention, a promoter, and transcriptional and
translational stop
signals. The various nucleotide and control sequences may be joined together
to produce a
recombinant expression vector that may include one or more (several)
convenient restriction
sites to allow for insertion or substitution of the polynucleotide encoding
the polypeptide at
such sites. Alternatively, the polynucleotide may be expressed by inserting
the
polynucleotide or a nucleic acid construct comprising the sequence into an
appropriate
vector for expression. In creating the expression vector, the coding sequence
is located in
the vector so that the coding sequence is operably linked with the appropriate
control
sequences for expression.
The recombinant expression vector may be any vector (e.g., a plasmid or virus)
that
can be conveniently subjected to recombinant DNA procedures and can bring
about
expression of the polynucleotide. The choice of the vector will typically
depend on the
compatibility of the vector with the host cell into which the vector is to be
introduced. The
vector may be a linear or closed circular plasmid.
The vector may be an autonomously replicating vector, i.e., a vector that
exists as an
extrachromosomal entity, the replication of which is independent of
chromosomal replication,
e.g., a plasmid, an extrachromosomal element, a minichromosome, or an
artificial
chromosome. The vector may contain any means for assuring self-replication.
Alternatively,
the vector may be one that, when introduced into the host cell, is integrated
into the genome
and replicated together with the chromosome(s) into which it has been
integrated.
Furthermore, a single vector or plasmid or two or more vectors or plasmids
that together
contain the total DNA to be introduced into the genome of the host cell, or a
transposon, may
be used.
The vector preferably contains one or more (several) selectable markers that
permit
easy selection of transformed, transfected, transduced, or the like cells. A
selectable marker
is a gene the product of which provides for biocide or viral resistance,
resistance to heavy
metals, prototrophy to auxotrophs, and the like.
Examples of bacterial selectable markers are the dal genes from Bacillus
subtilis or
-24-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
Bacillus licheniformis, or markers that confer antibiotic resistance such as
ampicillin,
chloramphenicol, kanamycin, or tetracycline resistance. Suitable markers for
yeast host cells
are ADE2, HIS3, LEU2, LYS2, MET3, TRP1, and URA3. Selectable markers for use
in a
filamentous fungal host cell include, but are not limited to, amdS
(acetamidase), argB
(ornithine carbamoyltransferase), bar (phosphinothricin acetyltransferase),
hph (hygromycin
phosphotransferase), niaD (nitrate reductase), pyrG (orotidine-5'-phosphate
decarboxylase),
sC (sulfate adenyltransferase), and trpC (anthranilate synthase), as well as
equivalents
thereof. Preferred for use in an Aspergillus cell are the amdS and pyrG genes
of Aspergillus
nidulans or Aspergillus oryzae and the bar gene of Streptomyces hygroscopicus.
The vector preferably contains an element(s) that permits integration of the
vector
into the host cell's genome or autonomous replication of the vector in the
cell independent of
the genome.
For integration into the host cell genome, the vector may rely on the
polynucleotide's
sequence encoding the polypeptide or any other element of the vector for
integration into the
genome by homologous or non-homologous recombination. Alternatively, the
vector may
contain additional polynucleotides for directing integration by homologous
recombination into
the genome of the host cell at a precise location(s) in the chromosome(s). To
increase the
likelihood of integration at a precise location, the integrational elements
should contain a
sufficient number of nucleic acids, such as 100 to 10,000 base pairs, 400 to
10,000 base
pairs, and 800 to 10,000 base pairs, which have a high degree of sequence
identity to the
corresponding target sequence to enhance the probability of homologous
recombination.
The integrational elements may be any sequence that is homologous with the
target
sequence in the genome of the host cell. Furthermore, the integrational
elements may be
non-encoding or encoding polynucleotides. On the other hand, the vector may be
integrated
into the genome of the host cell by non-homologous recombination.
For autonomous replication, the vector may further comprise an origin of
replication
enabling the vector to replicate autonomously in the host cell in question.
The origin of
replication may be any plasmid replicator mediating autonomous replication
that functions in
a cell. The term "origin of replication" or "plasmid replicator" means a
polynucleotide that
enables a plasmid or vector to replicate in vivo.
Examples of bacterial origins of replication are the origins of replication of
plasmids
pBR322, pUC19, pACYC177, and pACYC184 permitting replication in E. coli, and
pUB110,
pE194, pTA1060, and pAMR1 permitting replication in Bacillus.
Examples of origins of replication for use in a yeast host cell are the 2
micron origin
of replication, ARS1, ARS4, the combination of ARS1 and CEN3, and the
combination of
ARS4 and CEN6.
Examples of origins of replication useful in a filamentous fungal cell are
AMA1 and
-25-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
ANSI (Gems et al., 1991, Gene 98: 61-67; Cullen et al., 1987, Nucleic Acids
Res. 15: 9163-
9175; WO 00/24883). Isolation of the AMA1 gene and construction of plasmids or
vectors
comprising the gene can be accomplished according to the methods disclosed in
WO
00/24883.
More than one copy of a polynucleotide of the present invention may be
inserted into
a host cell to increase production of a polypeptide. An increase in the copy
number of the
polynucleotide can be obtained by integrating at least one additional copy of
the sequence
into the host cell genome or by including an amplifiable selectable marker
gene with the
polynucleotide where cells containing amplified copies of the selectable
marker gene, and
thereby additional copies of the polynucleotide, can be selected for by
cultivating the cells in
the presence of the appropriate selectable agent.
The procedures used to ligate the elements described above to construct the
recombinant expression vectors of the present invention are well known to one
skilled in the
art (see, e.g., Sambrook et al., 1989, supra).
Host Cells
The present invention also relates to recombinant host cells, comprising a
polynucleotide of the present invention operably linked to one or more
(several) control
sequences that direct the production of a polypeptide of the present
invention. A construct or
vector comprising a polynucleotide is introduced into a host cell so that the
construct or
vector is maintained as a chromosomal integrant or as a self-replicating extra-
chromosomal
vector as described earlier. The term "host cell" encompasses any progeny of a
parent cell
that is not identical to the parent cell due to mutations that occur during
replication. The
choice of a host cell will to a large extent depend upon the gene encoding the
polypeptide
and its source.
The host cell may be any cell useful in the recombinant production of a
polypeptide of
the present invention, e.g., a prokaryote or a eukaryote.
The prokaryotic host cell may be any gram-positive or gram-negative bacterium.
Gram-positive bacteria include, but not limited to, Bacillus, Clostridium,
Enterococcus,
Geobacillus, Lactobacillus, Lactococcus, Oceanobacillus, Staphylococcus,
Streptococcus,
and Streptomyces. Gram-negative bacteria include, but not limited to,
Campylobacter, E.
coli, Flavobacterium, Fusobacterium, Helicobacter, llyobacter, Neisseria,
Pseudomonas,
Salmonella, and Ureaplasma.
The bacterial host cell may be any Bacillus cell including, but not limited
to, Bacillus
alkalophilus, Bacillus amyloliquefaciens, Bacillus brevis, Bacillus circulans,
Bacillus clausii,
Bacillus coagulans, Bacillus firm us, Bacillus lautus, Bacillus lentus,
Bacillus licheniformis,
Bacillus megaterium, Bacillus pumilus, Bacillus stearothermophilus, Bacillus
subtilis, and
-26-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
Bacillus thuringiensis cells.
The bacterial host cell may also be any Streptococcus cell including, but not
limited
to, Streptococcus equisimilis, Streptococcus pyogenes, Streptococcus uberis,
and
Streptococcus equi subsp. Zooepidemicus cells.
The bacterial host cell may also be any Streptomyces cell including, but not
limited
to, Streptomyces achromogenes, Streptomyces avermitilis, Streptomyces
coelicolor,
Streptomyces griseus, and Streptomyces lividans cells.
The introduction of DNA into a Bacillus cell may, for instance, be effected by
protoplast transformation (see, e.g., Chang and Cohen, 1979, Mol. Gen. Genet.
168: 111-
115), by using competent cells (see, e.g., Young and Spizizen, 1961, J.
Bacteriol. 81: 823-
829, or Dubnau and Davidoff-Abelson, 1971, J. Mol. Biol. 56: 209-221), by
electroporation
(see, e.g., Shigekawa and Dower, 1988, Biotechniques 6: 742-751), or by
conjugation (see,
e.g., Koehler and Thorne, 1987, J. Bacteriol. 169: 5271-5278). The
introduction of DNA into
an E. coli cell may, for instance, be effected by protoplast transformation
(see, e.g.,
Hanahan, 1983, J. Mol. Biol. 166: 557-580) or electroporation (see, e.g.,
Dower et al., 1988,
Nucleic Acids Res. 16: 6127-6145). The introduction of DNA into a Streptomyces
cell may,
for instance, be effected by protoplast transformation and electroporation
(see, e.g., Gong et
al., 2004, Folia Microbiol. (Praha) 49: 399-405), by conjugation (see, e.g.,
Mazodier et al.,
1989, J. Bacteriol. 171: 3583-3585), or by transduction (see, e.g., Burke et
al., 2001, Proc.
Natl. Acad. Sci. USA 98: 6289-6294). The introduction of DNA into a
Pseudomonas cell
may, for instance, be effected by electroporation (see, e.g., Choi et al.,
2006, J. Microbiol.
Methods 64: 391-397) or by conjugation (see, e.g., Pinedo and Smets, 2005,
Appl. Environ.
Microbiol. 71: 51-57). The introduction of DNA into a Streptococcus cell may,
for instance, be
effected by natural competence (see, e.g., Perry and Kuramitsu, 1981, Infect.
Immun. 32:
1295-1297), by protoplast transformation (see, e.g., Catt and Jollick, 1991,
Microbios 68:
189-207), by electroporation (see, e.g., Buckley et al., 1999, Appl. Environ.
Microbiol. 65:
3800-3804) or by conjugation (see, e.g., Clewell, 1981, Microbiol. Rev. 45:
409-436).
However, any method known in the art for introducing DNA into a host cell can
be used.
The host cell may also be a eukaryote, such as a mammalian, insect, plant, or
fungal
cell.
The host cell may be a fungal cell. "Fungi" as used herein includes the phyla
Ascomycota, Basidiomycota, Chytridiomycota, and Zygomycota (as defined by
Hawksworth
et al., In, Ainsworth and Bisby's Dictionary of The Fungi, 8th edition, 1995,
CAB
International, University Press, Cambridge, UK) as well as the Oomycota (as
cited in
Hawksworth et al., 1995, supra, page 171) and all mitosporic fungi (Hawksworth
et al., 1995,
supra).
The fungal host cell may be a yeast cell. "Yeast" as used herein includes
-27-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
ascosporogenous yeast (Endomycetales), basidiosporogenous yeast, and yeast
belonging
to the Fungi Imperfecti (Blastomycetes). Since the classification of yeast may
change in the
future, for the purposes of this invention, yeast shall be defined as
described in Biology and
Activities of Yeast (Skinner, F.A., Passmore, S.M., and Davenport, R.R., eds,
Soc. App.
Bacteriol. Symposium Series No. 9, 1980).
The yeast host cell may be a Candida, Hansenula, Kluyveromyces, Pichia,
Saccharomyces, Schizosaccharomyces, or Yarrowia cell such as a Kluyveromyces
lactis,
Saccharomyces carlsbergensis, Saccharomyces cerevisiae, Saccharomyces
diastaticus,
Saccharomyces douglasii, Saccharomyces kluyveri, Saccharomyces norbensis,
Saccharomyces oviformis, or Yarrowia lipolytica cell.
The fungal host cell may be a filamentous fungal cell. "Filamentous fungi"
include all
filamentous forms of the subdivision Eumycota and Oomycota (as defined by
Hawksworth et
al., 1995, supra). The filamentous fungi are generally characterized by a
mycelial wall
composed of chitin, cellulose, glucan, chitosan, mannan, and other complex
polysaccharides. Vegetative growth is by hyphal elongation and carbon
catabolism is
obligately aerobic. In contrast, vegetative growth by yeasts such as
Saccharomyces
cerevisiae is by budding of a unicellular thallus and carbon catabolism may be
fermentative.
The filamentous fungal host cell may be an Acremonium, Aspergillus,
Aureobasidium, Bjerkandera, Ceriporiopsis, Chrysosporium, Coprinus, Coriolus,
Cryptococcus, Filibasidium, Fusarium, Humicola, Magnaporthe, Mucor,
Myceliophthora,
Neocallimastix, Neurospora, Paecilomyces, Penicillium, Phanerochaete, Phlebia,
Piromyces,
Pleurotus, Schizophyllum, Talaromyces, Thermoascus, Thielavia, Tolypocladium,
Trametes,
or Trichoderma cell.
For example, the filamentous fungal host cell may be an Aspergillus awamori,
Aspergillus foetidus, Aspergillus fumigatus, Aspergillus japonicus,
Aspergillus nidulans,
Aspergillus niger, Aspergillus oryzae, Bjerkandera adusta, Ceriporiopsis
aneirina,
Ceriporiopsis caregiea, Ceriporiopsis gilvescens, Ceriporiopsis pannocinta,
Ceriporiopsis
rivulosa, Ceriporiopsis subrufa, Ceriporiopsis subvermispora, Chrysosporium
inops,
Chrysosporium keratinophilum, Chrysosporium lucknowense, Chrysosporium
merdarium,
Chrysosporium pannicola, Chrysosporium queenslandicum, Chrysosporium tropicum,
Chrysosporium zonatum, Coprinus cinereus, Coriolus hirsutus, Fusarium
bactridioides,
Fusarium cerealis, Fusarium crookwellense, Fusarium culmorum, Fusarium
graminearum,
Fusarium graminum, Fusarium heterosporum, Fusarium negundi, Fusarium
oxysporum,
Fusarium reticulatum, Fusarium roseum, Fusarium sambucinum, Fusarium
sarcochroum,
Fusarium sporotrichioides, Fusarium sulphureum, Fusarium torulosum, Fusarium
trichothecioides, Fusarium venenatum, Humicola insolens, Humicola lanuginosa,
Mucor
miehei, Myceliophthora thermophila, Neurospora crassa, Penicillium
purpurogenum,
-28-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
Phanerochaete chrysosporium, Phlebia radiata, Pleurotus eryngii, Thielavia
terrestris,
Trametes villosa, Trametes versicolor, Trichoderma harzianum, Trichoderma
koningii,
Trichoderma longibrachiatum, Trichoderma reesei, or Trichoderma viride cell.
Fungal cells may be transformed by a process involving protoplast formation,
transformation of the protoplasts, and regeneration of the cell wall in a
manner known per
se. Suitable procedures for transformation of Aspergillus and Trichoderma host
cells are
described in EP 238023, Yelton et al., 1984, Proc. Natl. Acad. Sci. USA 81:
1470-1474, and
Christensen et al., 1988, Bio/Technology 6: 1419-1422. Suitable methods for
transforming
Fusarium species are described by Malardier et al., 1989, Gene 78: 147-156,
and WO
96/00787. Yeast may be transformed using the procedures described by Becker
and
Guarente, In Abelson, J.N. and Simon, M.I., editors, Guide to Yeast Genetics
and Molecular
Biology, Methods in Enzymology, Volume 194, pp 182-187, Academic Press, Inc.,
New
York; Ito et al., 1983, J. Bacteriol. 153: 163; and Hinnen et al., 1978, Proc.
Natl. Acad. Sci.
USA 75: 1920.
Methods of Production
The present invention also relates to methods of producing a polypeptide of
the
present invention, comprising: (a) cultivating a cell, which in its wild-type
form produces the
polypeptide, under conditions conducive for production of the polypeptide; and
(b) recovering
the polypeptide. In a preferred aspect, the cell is of the genus Aspergillus.
In a more
preferred aspect, the cell is Aspergillus aculeatus. In a most preferred
aspect, the cell is
Aspergillus aculeatus IAM 2445.
The present invention also relates to methods of producing a polypeptide of
the
present invention, comprising: (a) cultivating a recombinant host cell of the
present invention
under conditions conducive for production of the polypeptide; and (b)
recovering the
polypeptide.
The host cells are cultivated in a nutrient medium suitable for production of
the
polypeptide using methods well known in the art. For example, the cell may be
cultivated by
shake flask cultivation, and small-scale or large-scale fermentation
(including continuous,
batch, fed-batch, or solid state fermentations) in laboratory or industrial
fermentors
performed in a suitable medium and under conditions allowing the polypeptide
to be
expressed and/or isolated. The cultivation takes place in a suitable nutrient
medium
comprising carbon and nitrogen sources and inorganic salts, using procedures
known in the
art. Suitable media are available from commercial suppliers or may be prepared
according to
published compositions (e.g., in catalogues of the American Type Culture
Collection). If the
polypeptide is secreted into the nutrient medium, the polypeptide can be
recovered directly
from the medium. If the polypeptide is not secreted, it can be recovered from
cell lysates.
-29-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
The polypeptide may be detected using methods known in the art that are
specific for
the polypeptides. These detection methods may include use of specific
antibodies, formation
of an enzyme product, or disappearance of an enzyme substrate. For example, an
enzyme
assay may be used to determine the activity of the polypeptide.
The polypeptide may be recovered using methods known in the art. For example,
the
polypeptide may be recovered from the nutrient medium by conventional
procedures
including, but not limited to, centrifugation, filtration, extraction, spray-
drying, evaporation, or
precipitation.
The polypeptide may be purified by a variety of procedures known in the art
including, but not limited to, chromatography (e.g., ion exchange, affinity,
hydrophobic,
chromatofocusing, and size exclusion), electrophoretic procedures (e.g.,
preparative
isoelectric focusing), differential solubility (e.g., ammonium sulfate
precipitation), SDS-
PAGE, or extraction (see, e.g., Protein Purification, J.-C. Janson and Lars
Ryden, editors,
VCH Publishers, New York, 1989) to obtain substantially pure polypeptides.
In an alternative aspect, the polypeptide is not recovered, but rather a host
cell of the
present invention expressing the polypeptide is used as a source of the
polypeptide.
Plants
The present invention also relates to isolated plants, e.g., a transgenic
plant, plant
part, or plant cell, comprising an isolated polynucleotide of the present
invention so as to
express and produce the polypeptide in recoverable quantities. The polypeptide
may be
recovered from the plant or plant part. Alternatively, the plant or plant part
containing the
polypeptide may be used as such for improving the quality of a food or feed,
e.g., improving
nutritional value, palatability, and rheological properties, or to destroy an
antinutritive factor.
The transgenic plant can be dicotyledonous (a dicot) or monocotyledonous (a
monocot). Examples of monocot plants are grasses, such as meadow grass (blue
grass,
Poa), forage grass such as Festuca, Lolium, temperate grass, such as Agrostis,
and cereals,
e.g., wheat, oats, rye, barley, rice, sorghum, and maize (corn).
Examples of dicot plants are tobacco, legumes, such as lupins, potato, sugar
beet,
pea, bean and soybean, and cruciferous plants (family Brassicaceae), such as
cauliflower,
rape seed, and the closely related model organism Arabidopsis thaliana.
Examples of plant parts are stem, callus, leaves, root, fruits, seeds, and
tubers as
well as the individual tissues comprising these parts, e.g., epidermis,
mesophyll,
parenchyme, vascular tissues, meristems. Specific plant cell compartments,
such as
chloroplasts, apoplasts, mitochondria, vacuoles, peroxisomes and cytoplasm are
also
considered to be a plant part. Furthermore, any plant cell, whatever the
tissue origin, is
considered to be a plant part. Likewise, plant parts such as specific tissues
and cells isolated
-30-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
to facilitate the utilization of the invention are also considered plant
parts, e.g., embryos,
endosperms, aleurone and seeds coats.
Also included within the scope of the present invention are the progeny of
such
plants, plant parts, and plant cells.
The transgenic plant or plant cell expressing a polypeptide may be constructed
in
accordance with methods known in the art. In short, the plant or plant cell is
constructed by
incorporating one or more (several) expression constructs encoding a
polypeptide into the
plant host genome or chloroplast genome and propagating the resulting modified
plant or
plant cell into a transgenic plant or plant cell.
The expression construct is conveniently a nucleic acid construct that
comprises a
polynucleotide encoding a polypeptide operably linked with appropriate
regulatory
sequences required for expression of the polynucleotide in the plant or plant
part of choice.
Furthermore, the expression construct may comprise a selectable marker useful
for
identifying host cells into which the expression construct has been integrated
and DNA
sequences necessary for introduction of the construct into the plant in
question (the latter
depends on the DNA introduction method to be used).
The choice of regulatory sequences, such as promoter and terminator sequences
and optionally signal or transit sequences, is determined, for example, on the
basis of when,
where, and how the polypeptide is desired to be expressed. For instance, the
expression of
the gene encoding a polypeptide may be constitutive or inducible, or may be
developmental,
stage or tissue specific, and the gene product may be targeted to a specific
tissue or plant
part such as seeds or leaves. Regulatory sequences are, for example, described
by Tague
et al., 1988, Plant Physiology 86: 506.
For constitutive expression, the 35S-CaMV, the maize ubiquitin 1, and the rice
actin 1
promoter may be used (Franck et al., 1980, Cell 21: 285-294; Christensen et
al., 1992, Plant
Mol. Biol. 18: 675-689; Zhang et al., 1991, Plant Cell 3: 1155-1165). Organ-
specific
promoters may be, for example, a promoter from storage sink tissues such as
seeds, potato
tubers, and fruits (Edwards and Coruzzi, 1990, Ann. Rev. Genet. 24: 275-303),
or from
metabolic sink tissues such as meristems (Ito et al., 1994, Plant Mol. Biol.
24: 863-878), a
seed specific promoter such as the glutelin, prolamin, globulin, or albumin
promoter from rice
(Wu et al., 1998, Plant Cell Physiol. 39: 885-889), a Vicia faba promoter from
the legumin B4
and the unknown seed protein gene from Vicia faba (Conrad et al., 1998, J.
Plant Physiol.
152: 708-711), a promoter from a seed oil body protein (Chen et al., 1998,
Plant Cell
Physiol. 39: 935-941), the storage protein napA promoter from Brassica napus,
or any other
seed specific promoter known in the art, e.g., as described in WO 91/14772.
Furthermore,
the promoter may be a leaf specific promoter such as the rbcs promoter from
rice or tomato
(Kyozuka et al., 1993, Plant Physiol. 102: 991-1000), the chlorella virus
adenine
-31-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
methyltransferase gene promoter (Mitra and Higgins, 1994, Plant Mol. Biol. 26:
85-93), the
aldP gene promoter from rice (Kagaya et al., 1995, Mol. Gen. Genet. 248: 668-
674), or a
wound inducible promoter such as the potato pin2 promoter (Xu et al., 1993,
Plant Mol. Biol.
22: 573-588). Likewise, the promoter may inducible by abiotic treatments such
as
temperature, drought, or alterations in salinity or induced by exogenously
applied
substances that activate the promoter, e.g., ethanol, oestrogens, plant
hormones such as
ethylene, abscisic acid, and gibberellic acid, and heavy metals.
A promoter enhancer element may also be used to achieve higher expression of a
polypeptide in the plant. For instance, the promoter enhancer element may be
an intron that
is placed between the promoter and the polynucleotide encoding a polypeptide.
For
instance, Xu et al., 1993, supra, disclose the use of the first intron of the
rice actin 1 gene to
enhance expression.
The selectable marker gene and any other parts of the expression construct may
be
chosen from those available in the art.
The nucleic acid construct is incorporated into the plant genome according to
conventional techniques known in the art, including Agrobacterium-mediated
transformation,
virus-mediated transformation, microinjection, particle bombardment, biolistic
transformation,
and electroporation (Gasser et al., 1990, Science 244: 1293; Potrykus, 1990,
Bio/Technology 8: 535; Shimamoto et al., 1989, Nature 338: 274).
Presently, Agrobacterium tumefaciens-mediated gene transfer is the method of
choice for generating transgenic dicots (for a review, see Hooykas and
Schilperoort, 1992,
Plant Mol. Biol. 19: 15-38) and can also be used for transforming monocots,
although other
transformation methods are often used for these plants. Presently, the method
of choice for
generating transgenic monocots is particle bombardment (microscopic gold or
tungsten
particles coated with the transforming DNA) of embryonic calli or developing
embryos
(Christou, 1992, Plant J. 2: 275-281; Shimamoto, 1994, Curr. Opin. Biotechnol.
5: 158-162;
Vasil et al., 1992, Bio/Technology 10: 667-674). An alternative method for
transformation of
monocots is based on protoplast transformation as described by Omirulleh et
al., 1993, Plant
Mol. Biol. 21: 415-428. Additional transformation methods for use in
accordance with the
present disclosure include those described in U.S. Patent Nos. 6,395,966 and
7,151,204
(both of which are herein incorporated by reference in their entirety).
Following transformation, the transformants having incorporated the expression
construct are selected and regenerated into whole plants according to methods
well known
in the art. Often the transformation procedure is designed for the selective
elimination of
selection genes either during regeneration or in the following generations by
using, for
example, co-transformation with two separate T-DNA constructs or site specific
excision of
the selection gene by a specific recombinase.
-32-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
In addition to direct transformation of a particular plant genotype with a
construct
prepared according to the present invention, transgenic plants may be made by
crossing a
plant having the construct to a second plant lacking the construct. For
example, a construct
encoding a polypeptide can be introduced into a particular plant variety by
crossing, without
the need for ever directly transforming a plant of that given variety.
Therefore, the present
invention encompasses not only a plant directly regenerated from cells which
have been
transformed in accordance with the present invention, but also the progeny of
such plants.
As used herein, progeny may refer to the offspring of any generation of a
parent plant
prepared in accordance with the present invention. Such progeny may include a
DNA
construct prepared in accordance with the present invention, or a portion of a
DNA construct
prepared in accordance with the present invention. Crossing results in the
introduction of a
transgene into a plant line by cross pollinating a starting line with a donor
plant line. Non-
limiting examples of such steps are further articulated in U.S. Patent No.
7,151,204.
Plants may be generated through a process of backcross conversion. For
example,
plants include plants referred to as a backcross converted genotype, line,
inbred, or hybrid.
Genetic markers may be used to assist in the introgression of one or more
transgenes of the invention from one genetic background into another. Marker
assisted
selection offers advantages relative to conventional breeding in that it can
be used to avoid
errors caused by phenotypic variations. Further, genetic markers may provide
data regarding
the relative degree of elite germplasm in the individual progeny of a
particular cross. For
example, when a plant with a desired trait which otherwise has a non-
agronomically
desirable genetic background is crossed to an elite parent, genetic markers
may be used to
select progeny which not only possess the trait of interest, but also have a
relatively large
proportion of the desired germplasm. In this way, the number of generations
required to
introgress one or more traits into a particular genetic background is
minimized.
The present invention also relates to methods of producing a polypeptide of
the
present invention comprising: (a) cultivating a transgenic plant or a plant
cell comprising a
polynucleotide encoding the polypeptide under conditions conducive for
production of the
polypeptide; and (b) recovering the polypeptide.
Removal or Reduction of Cellobiohydrolase Activity
The present invention also relates to methods of producing a mutant of a
parent cell,
which comprises disrupting or deleting a polynucleotide, or a portion thereof,
encoding a
polypeptide of the present invention, which results in the mutant cell
producing less of the
polypeptide than the parent cell when cultivated under the same conditions.
The mutant cell may be constructed by reducing or eliminating expression of
the
polynucleotide using methods well known in the art, for example, insertions,
disruptions,
-33-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
replacements, or deletions. In a preferred aspect, the polynucleotide is
inactivated. The
polynucleotide to be modified or inactivated may be, for example, the coding
region or a part
thereof essential for activity, or a regulatory element required for the
expression of the
coding region. An example of such a regulatory or control sequence may be a
promoter
sequence or a functional part thereof, i.e., a part that is sufficient for
affecting expression of
the polynucleotide. Other control sequences for possible modification include,
but are not
limited to, a leader, polyadenylation sequence, propeptide sequence, signal
peptide
sequence, transcription terminator, and transcriptional activator.
Modification or inactivation of the polynucleotide may be performed by
subjecting the
parent cell to mutagenesis and selecting for mutant cells in which expression
of the
polynucleotide has been reduced or eliminated. The mutagenesis, which may be
specific or
random, may be performed, for example, by use of a suitable physical or
chemical
mutagenizing agent, by use of a suitable oligonucleotide, or by subjecting the
DNA
sequence to PCR generated mutagenesis. Furthermore, the mutagenesis may be
performed
by use of any combination of these mutagenizing agents.
Examples of a physical or chemical mutagenizing agent suitable for the present
purpose include ultraviolet (UV) irradiation, hydroxylamine, N-methyl-N'-nitro-
N-nitrosoguanidine (MNNG), O-methyl hydroxylamine, nitrous acid, ethyl methane
sulphonate (EMS), sodium bisulphite, formic acid, and nucleotide analogues.
When such agents are used, the mutagenesis is typically performed by
incubating
the parent cell to be mutagenized in the presence of the mutagenizing agent of
choice under
suitable conditions, and screening and/or selecting for mutant cells
exhibiting reduced or no
expression of the gene.
Modification or inactivation of the polynucleotide may be accomplished by
introduction, substitution, or removal of one or more (several) nucleotides in
the gene or a
regulatory element required for the transcription or translation thereof. For
example,
nucleotides may be inserted or removed so as to result in the introduction of
a stop codon,
the removal of the start codon, or a change in the open reading frame. Such
modification or
inactivation may be accomplished by site-directed mutagenesis or PCR generated
mutagenesis in accordance with methods known in the art. Although, in
principle, the
modification may be performed in vivo, i.e., directly on the cell expressing
the polynucleotide
to be modified, it is preferred that the modification be performed in vitro as
exemplified
below.
An example of a convenient way to eliminate or reduce expression of a
polynucleotide is based on techniques of gene replacement, gene deletion, or
gene
disruption. For example, in the gene disruption method, a nucleic acid
sequence
corresponding to the endogenous polynucleotide is mutagenized in vitro to
produce a
-34-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
defective nucleic acid sequence that is then transformed into the parent cell
to produce a
defective gene. By homologous recombination, the defective nucleic acid
sequence replaces
the endogenous polynucleotide. It may be desirable that the defective
polynucleotide also
encodes a marker that may be used for selection of transformants in which the
polynucleotide has been modified or destroyed. In a particularly preferred
aspect, the
polynucleotide is disrupted with a selectable marker such as those described
herein.
The present invention also relates to methods of inhibiting the expression of
a
polypeptide having cellobiohydrolase activity in a cell, comprising
administering to the cell or
expressing in the cell a double-stranded RNA (dsRNA) molecule, wherein the
dsRNA
comprises a subsequence of a polynucleotide of the present invention. In a
preferred aspect,
the dsRNA is about 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or more duplex
nucleotides in
length.
The dsRNA is preferably a small interfering RNA (mRNA) or a micro RNA (miRNA).
In a preferred aspect, the dsRNA is small interfering RNA (siRNAs) for
inhibiting
transcription. In another preferred aspect, the dsRNA is micro RNA (miRNAs)
for inhibiting
translation.
The present invention also relates to such double-stranded RNA (dsRNA)
molecules,
comprising a portion of the mature polypeptide coding sequence of SEQ ID NO: 1
for
inhibiting expression of the polypeptide in a cell. While the present
invention is not limited by
any particular mechanism of action, the dsRNA can enter a cell and cause the
degradation
of a single-stranded RNA (ssRNA) of similar or identical sequences, including
endogenous
mRNAs. When a cell is exposed to dsRNA, mRNA from the homologous gene is
selectively
degraded by a process called RNA interference (RNAi).
The dsRNAs of the present invention can be used in gene-silencing. In one
aspect,
the invention provides methods to selectively degrade RNA using a dsRNAi of
the present
invention. The process may be practiced in vitro, ex vivo or in vivo. In one
aspect, the
dsRNA molecules can be used to generate a loss-of-function mutation in a cell,
an organ or
an animal. Methods for making and using dsRNA molecules to selectively degrade
RNA are
well known in the art; see, for example, U.S. Patent Nos. 6,489,127;
6,506,559; 6,511,824;
and 6,515,109.
The present invention further relates to a mutant cell of a parent cell that
comprises a
disruption or deletion of a polynucleotide encoding the polypeptide or a
control sequence
thereof or a silenced gene encoding the polypeptide, which results in the
mutant cell
producing less of the polypeptide or no polypeptide compared to the parent
cell.
The polypeptide-deficient mutant cells are particularly useful as host cells
for the
expression of native and heterologous polypeptides. Therefore, the present
invention further
relates to methods of producing a native or heterologous polypeptide,
comprising: (a)
-35-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
cultivating the mutant cell under conditions conducive for production of the
polypeptide; and
(b) recovering the polypeptide. The term "heterologous polypeptides" means
polypeptides
that are not native to the host cell, e.g., a variant of a native protein. The
host cell may
comprise more than one copy of a polynucleotide encoding the native or
heterologous
polypeptide.
The methods used for cultivation and purification of the product of interest
may be
performed by methods known in the art.
The methods of the present invention for producing an essentially
cellobiohydrolase-
free product is of particular interest in the production of eukaryotic
polypeptides, in particular
fungal proteins such as enzymes. The cellobiohydrolase-deficient cells may
also be used to
express heterologous proteins of pharmaceutical interest such as hormones,
growth factors,
receptors, and the like. The term "eukaryotic polypeptides" includes not only
native
polypeptides, but also those polypeptides, e.g., enzymes, which have been
modified by
amino acid substitutions, deletions or additions, or other such modifications
to enhance
activity, thermostability, pH tolerance and the like.
In a further aspect, the present invention relates to a protein product
essentially free
from cellobiohydrolase activity that is produced by a method of the present
invention.
Compositions
The present invention also relates to compositions comprising a polypeptide of
the
present invention.
The composition may comprise a polypeptide of the present invention as the
major
enzymatic component, e.g., a mono-component composition. Alternatively, the
composition
may comprise multiple enzymatic activities, such as one or more (several)
enzymes selected
from the group consisting of a cellulase, a GH61 polypeptide having
cellulolytic enhancing
activity, a hemicellulase, an expansin, an esterase, a laccase, a ligninolytic
enzyme, a
pectinase, a peroxidase, a protease, and a swollenin.
The polypeptide compositions may be prepared in accordance with methods known
in the art and may be in the form of a liquid or a dry composition. For
instance, the
polypeptide composition may be in the form of a granulate or a microgranulate.
The
polypeptide to be included in the composition may be stabilized in accordance
with methods
known in the art.
Examples are given below of preferred uses of the polypeptide compositions of
the
invention. The dosage of the polypeptide composition of the invention and
other conditions
under which the composition is used may be determined on the basis of methods
known in
the art.
-36-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
Uses
The present invention is also directed to the following methods for using the
polypeptides, or compositions thereof.
The present invention also relates to methods for degrading or converting a
cellulosic
material, comprising: treating the cellulosic material with an enzyme
composition in the
presence of a polypeptide of the present invention. In one aspect, the method
above further
comprises recovering the degraded or converted cellulosic material. Soluble
products of
degradation or conversion of the cellulosic material can be separated from the
insoluble
cellulosic material using technology well known in the art such as, for
example,
centrifugation, filtration, and gravity settling.
The present invention also relates to methods for producing a fermentation
product,
comprising: (a) saccharifying a cellulosic material with an enzyme composition
in the
presence of a polypeptide of the present invention; (b) fermenting the
saccharified cellulosic
material with one or more (several) fermenting microorganisms to produce the
fermentation
product; and (c) recovering the fermentation product from the fermentation.
The present invention also relates to methods of fermenting a cellulosic
material,
comprising: fermenting the cellulosic material with one or more (several)
fermenting
microorganisms, wherein the cellulosic material is saccharified with an enzyme
composition
in the presence of a polypeptide of the present invention. In one aspect, the
fermenting of the
cellulosic material produces a fermentation product. In another aspect, the
method further
comprises recovering the fermentation product from the fermentation.
The processing of the cellulosic material according to the present invention
can be
accomplished using processes conventional in the art. Moreover, the methods of
the present
invention can be implemented using any conventional biomass processing
apparatus
configured to operate in accordance with the invention.
Hydrolysis (saccharification) and fermentation, separate or simultaneous,
include, but
are not limited to, separate hydrolysis and fermentation (SHF); simultaneous
saccharification
and fermentation (SSF); simultaneous saccharification and cofermentation
(SSCF); hybrid
hydrolysis and fermentation (HHF); separate hydrolysis and co-fermentation
(SHCF); hybrid
hydrolysis and co-fermentation (HHCF); and direct microbial conversion (DMC).
SHF uses
separate process steps to first enzymatically hydrolyze cellulosic material to
fermentable
sugars, e.g., glucose, cellobiose, cellotriose, and pentose sugars, and then
ferment the
fermentable sugars to ethanol. In SSF, the enzymatic hydrolysis of the
cellulosic material
and the fermentation of sugars to ethanol are combined in one step
(Philippidis, G. P., 1996,
Cellulose bioconversion technology, in Handbook on Bioethanol: Production and
Utilization,
Wyman, C. E., ed., Taylor & Francis, Washington, DC, 179-212). SSCF involves
the
cofermentation of multiple sugars (Sheehan, J., and Himmel, M., 1999, Enzymes,
energy
-37-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
and the environment: A strategic perspective on the U.S. Department of
Energy's research
and development activities for bioethanol, Biotechnol. Prog. 15: 817-827). HHF
involves a
separate hydrolysis step, and in addition a simultaneous saccharification and
hydrolysis
step, which can be carried out in the same reactor. The steps in an HHF
process can be
carried out at different temperatures, i.e., high temperature enzymatic
saccharification
followed by SSF at a lower temperature that the fermentation strain can
tolerate. DMC
combines all three processes (enzyme production, hydrolysis, and fermentation)
in one or
more (several) steps where the same organism is used to produce the enzymes
for
conversion of the cellulosic material to fermentable sugars and to convert the
fermentable
sugars into a final product (Lynd, L. R., Weimer, P. J., van Zyl, W. H., and
Pretorius, I. S.,
2002, Microbial cellulose utilization: Fundamentals and biotechnology,
Microbiol. Mol. Biol.
Reviews 66: 506-577). It is understood herein that any method known in the art
comprising
pretreatment, enzymatic hydrolysis (saccharification), fermentation, or a
combination thereof,
can be used in the practicing the methods of the present invention.
A conventional apparatus can include a fed-batch stirred reactor, a batch
stirred
reactor, a continuous flow stirred reactor with ultrafiltration, and/or a
continuous plug-flow
column reactor (Fernanda de Castilhos Corazza, Flavio Faria de Moraes, Gisella
Maria
Zanin and No Neitzel, 2003, Optimal control in fed-batch reactor for the
cellobiose
hydrolysis, Acta Scientiarum. Technology 25: 33-38; Gusakov, A. V., and
Sinitsyn, A. P.,
1985, Kinetics of the enzymatic hydrolysis of cellulose: 1. A mathematical
model for a batch
reactor process, Enz. Microb. Technol. 7: 346-352), an attrition reactor (Ryu,
S. K., and Lee,
J. M., 1983, Bioconversion of waste cellulose by using an attrition
bioreactor, Biotechnol.
Bioeng. 25: 53-65), or a reactor with intensive stirring induced by an
electromagnetic field
(Gusakov, A. V., Sinitsyn, A. P., Davydkin, I. Y., Davydkin, V. Y., Protas, O.
V., 1996,
Enhancement of enzymatic cellulose hydrolysis using a novel type of bioreactor
with
intensive stirring induced by electromagnetic field, Appl. Biochem.
Biotechnol. 56: 141-153).
Additional reactor types include: fluidized bed, upflow blanket, immobilized,
and extruder
type reactors for hydrolysis and/or fermentation.
Pretreatment. In practicing the methods of the present invention, any
pretreatment
process known in the art can be used to disrupt plant cell wall components of
the cellulosic
material (Chandra et al., 2007, Substrate pretreatment: The key to effective
enzymatic
hydrolysis of lignocellulosics? Adv. Biochem. Engin./Biotechnol. 108: 67-93;
Galbe and
Zacchi, 2007, Pretreatment of lignocellulosic materials for efficient
bioethanol production,
Adv. Biochem. Engin. /Biotechnol. 108: 41-65; Hendriks and Zeeman, 2009,
Pretreatments
to enhance the digestibility of lignocellulosic biomass, Bioresource Technol.
100: 10-18;
Mosier et al., 2005, Features of promising technologies for pretreatment of
lignocellulosic
biomass, Bioresource Technol. 96: 673-686; Taherzadeh and Karimi, 2008,
Pretreatment of
-38-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
lignocellulosic wastes to improve ethanol and biogas production: A review,
Int. J. of Mol. Sci.
9: 1621-1651; Yang and Wyman, 2008, Pretreatment: the key to unlocking low-
cost
cellulosic ethanol, Biofuels Bioproducts and Biorefining-Biofpr. 2: 26-40).
The cellulosic material can also be subjected to particle size reduction, pre-
soaking,
wetting, washing, and/or conditioning prior to pretreatment using methods
known in the art.
Conventional pretreatments include, but are not limited to, steam pretreatment
(with
or without explosion), dilute acid pretreatment, hot water pretreatment,
alkaline pretreatment,
lime pretreatment, wet oxidation, wet explosion, ammonia fiber explosion,
organosolv
pretreatment, and biological pretreatment. Additional pretreatments include
ammonia
percolation, ultrasound, electroporation, microwave, supercritical C02,
supercritical H2O,
ozone, and gamma irradiation pretreatments.
The cellulosic material can be pretreated before hydrolysis and/or
fermentation.
Pretreatment is preferably performed prior to the hydrolysis. Alternatively,
the pretreatment can
be carried out simultaneously with enzyme hydrolysis to release fermentable
sugars, such as
glucose, xylose, and/or cellobiose. In most cases the pretreatment step itself
results in some
conversion of the cellulosic material to fermentable sugars (even in absence
of enzymes).
Steam Pretreatment: In steam pretreatment, cellulosic material is heated to
disrupt
the plant cell wall components, including lignin, hemicellulose, and cellulose
to make the
cellulose and other fractions, e.g., hemicellulose, accessible to enzymes.
Cellulosic material
is passed to or through a reaction vessel where steam is injected to increase
the
temperature to the required temperature and pressure and is retained therein
for the desired
reaction time. Steam pretreatment is preferably done at 140-230 C, more
preferably 160-
200 C, and most preferably 170-190 C, where the optimal temperature range
depends on
any addition of a chemical catalyst. Residence time for the steam pretreatment
is preferably
1-15 minutes, more preferably 3-12 minutes, and most preferably 4-10 minutes,
where the
optimal residence time depends on temperature range and any addition of a
chemical
catalyst. Steam pretreatment allows for relatively high solids loadings, so
that cellulosic
material is generally only moist during the pretreatment. The steam
pretreatment is often
combined with an explosive discharge of the material after the pretreatment,
which is known
as steam explosion, that is, rapid flashing to atmospheric pressure and
turbulent flow of the
material to increase the accessible surface area by fragmentation (Duff and
Murray, 1996,
Bioresource Technology 855: 1-33; Galbe and Zacchi, 2002, Appl. Microbiol.
Biotechnol. 59:
618-628; U.S. Patent Application No. 20020164730). During steam pretreatment,
hemicellulose acetyl groups are cleaved and the resulting acid autocatalyzes
partial
hydrolysis of the hemicellulose to monosaccharides and oligosaccharides.
Lignin is removed
to only a limited extent.
A catalyst such as H2SO4 or SO2 (typically 0.3 to 3% w/w) is often added prior
to
-39-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
steam pretreatment, which decreases the time and temperature, increases the
recovery, and
improves enzymatic hydrolysis (Ballesteros et al., 2006, App!. Biochem.
Biotechnol. 129-
132: 496-508; Varga et al., 2004, Appl. Biochem. Biotechnol. 113-116: 509-523;
Sassner et
al., 2006, Enzyme Microb. Technol. 39: 756-762).
Chemical Pretreatment: The term "chemical treatment" refers to any chemical
pretreatment that promotes the separation and/or release of cellulose,
hemicellulose, and/or
lignin. Examples of suitable chemical pretreatment processes include, for
example, dilute acid
pretreatment, lime pretreatment, wet oxidation, ammonia fiber/freeze explosion
(AFEX),
ammonia percolation (APR), and organosolv pretreatments.
In dilute acid pretreatment, cellulosic material is mixed with dilute acid,
typically H2SO4,
and water to form a slurry, heated by steam to the desired temperature, and
after a
residence time flashed to atmospheric pressure. The dilute acid pretreatment
can be
performed with a number of reactor designs, e.g., plug-flow reactors, counter-
current reactors,
or continuous counter-current shrinking bed reactors (Duff and Murray, 1996,
supra; Schell et
a!., 2004, Bioresource Technol. 91: 179-188; Lee et a!., 1999, Adv. Biochem.
Eng. Biotechnol.
65: 93-115).
Several methods of pretreatment under alkaline conditions can also be used.
These
alkaline pretreatments include, but are not limited to, lime pretreatment, wet
oxidation, ammonia
percolation (APR), and ammonia fiber/freeze explosion (AFEX).
Lime pretreatment is performed with calcium carbonate, sodium hydroxide, or
ammonia
at low temperatures of 85-150 C and residence times from 1 hour to several
days (Wyman et
a!., 2005, Bioresource Technol. 96: 1959-1966; Mosier et a!., 2005,
Bioresource Technol. 96:
673-686). WO 2006/110891, WO 2006/11899, WO 2006/11900, and WO 2006/110901
disclose pretreatment methods using ammonia.
Wet oxidation is a thermal pretreatment performed typically at 180-200 C for 5-
15
minutes with addition of an oxidative agent such as hydrogen peroxide or over-
pressure of
oxygen (Schmidt and Thomsen, 1998, Bioresource Technol. 64: 139-151; Palonen
et a!., 2004,
Appl. Biochem. Biotechnol. 117: 1-17; Varga et a!., 2004, Biotechnol. Bioeng.
88: 567-574;
Martin et a!., 2006, J. Chem. Technol. Biotechnol. 81: 1669-1677). The
pretreatment is
performed at preferably 1-40% dry matter, more preferably 2-30% dry matter,
and most
preferably 5-20% dry matter, and often the initial pH is increased by the
addition of alkali such
as sodium carbonate.
A modification of the wet oxidation pretreatment method, known as wet
explosion
(combination of wet oxidation and steam explosion), can handle dry matter up
to 30%. In wet
explosion, the oxidizing agent is introduced during pretreatment after a
certain residence time.
The pretreatment is then ended by flashing to atmospheric pressure (WO
2006/032282).
Ammonia fiber explosion (AFEX) involves treating cellulosic material with
liquid or
-40-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
gaseous ammonia at moderate temperatures such as 90-100 C and high pressure
such as 17-
20 bar for 5-10 minutes, where the dry matter content can be as high as 60%
(Gollapalli et a!.,
2002, App!. Biochem. Biotechnol. 98: 23-35; Chundawat et a!., 2007,
Biotechnol. Bioeng. 96:
219-231; Alizadeh et al., 2005, App!. Biochem. Biotechnol. 121: 1133-1141;
Teymouri et a!.,
2005, Bioresource Technol. 96: 2014-2018). AFEX pretreatment results in the
depolymerization
of cellulose and partial hydrolysis of hemicellulose. Lignin-carbohydrate
complexes are cleaved.
Organosolv pretreatment delignifies cellulosic material by extraction using
aqueous
ethanol (40-60% ethanol) at 160-200 C for 30-60 minutes (Pan et a!., 2005,
Biotechnol. Bioeng.
90: 473-481; Pan et a!., 2006, Biotechnol. Bioeng. 94: 851-861; Kurabi et a!.,
2005, App!.
Biochem. Biotechnol. 121: 219-230). Sulphuric acid is usually added as a
catalyst. In
organosolv pretreatment, the majority of hemicellulose is removed.
Other examples of suitable pretreatment methods are described by Schell et
a!., 2003,
App!. Biochem. and Biotechnol. Vol. 105-108, p. 69-85, and Mosier et al.,
2005, Bioresource
Technology 96: 673-686, and U.S. Published Application 2002/0164730.
In one aspect, the chemical pretreatment is preferably carried out as an acid
treatment,
and more preferably as a continuous dilute and/or mild acid treatment. The
acid is typically
sulfuric acid, but other acids can also be used, such as acetic acid, citric
acid, nitric acid,
phosphoric acid, tartaric acid, succinic acid, hydrogen chloride, or mixtures
thereof. Mild acid
treatment is conducted in the pH range of preferably 1-5, more preferably 1-4,
and most
preferably 1-3. In one aspect, the acid concentration is in the range from
preferably 0.01 to 20
wt % acid, more preferably 0.05 to 10 wt % acid, even more preferably 0.1 to 5
wt % acid, and
most preferably 0.2 to 2.0 wt % acid. The acid is contacted with cellulosic
material and held at a
temperature in the range of preferably 160-220 C, and more preferably 165-195
C, for periods
ranging from seconds to minutes to, e.g., 1 second to 60 minutes.
In another aspect, pretreatment is carried out as an ammonia fiber explosion
step
(AFEX pretreatment step).
In another aspect, pretreatment takes place in an aqueous slurry. In preferred
aspects, cellulosic material is present during pretreatment in amounts
preferably between
10-80 wt %, more preferably between 20-70 wt %, and most preferably between 30-
60 wt %,
such as around 50 wt %. The pretreated cellulosic material can be unwashed or
washed
using any method known in the art, e.g., washed with water.
Mechanical Pretreatment: The term "mechanical pretreatment" refers to various
types of
grinding or milling (e.g., dry milling, wet milling, or vibratory ball
milling).
Physical Pretreatment: The term "physical pretreatment" refers to any
pretreatment that
promotes the separation and/or release of cellulose, hemicellulose, and/or
lignin from the
cellulosic material. For example, physical pretreatment can involve
irradiation (e.g., microwave
irradiation), steaming/steam explosion, hydrothermolysis, and combinations
thereof.
-41 -
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
Physical pretreatment can involve high pressure and/or high temperature (steam
explosion). In one aspect, high pressure means pressure in the range of
preferably about 300
to about 600 psi, more preferably about 350 to about 550 psi, and most
preferably about 400 to
about 500 psi, such as around 450 psi. In another aspect, high temperature
means
temperatures in the range of about 100 to about 300 C, preferably about 140 to
about 235 C. In
a preferred aspect, mechanical pretreatment is performed in a batch-process,
steam gun
hydrolyzer system that uses high pressure and high temperature as defined
above, e.g., a
Sunds Hydrolyzer available from Sunds Defibrator AB, Sweden.
Combined Physical and Chemical Pretreatment: Cellulosic material can be
pretreated
both physically and chemically. For instance, the pretreatment step can
involve dilute or mild
acid treatment and high temperature and/or pressure treatment. The physical
and chemical
pretreatments can be carried out sequentially or simultaneously, as desired. A
mechanical
pretreatment can also be included.
Accordingly, in a preferred aspect, the cellulosic material is subjected to
mechanical,
chemical, or physical pretreatment, or any combination thereof, to promote the
separation
and/or release of cellulose, hemicellulose, and/or lignin.
Biological Pretreatment: The term "biological pretreatment" refers to any
biological
pretreatment that promotes the separation and/or release of cellulose,
hemicellulose, and/or
lignin from the cellulosic material. Biological pretreatment techniques can
involve applying
lignin-solubilizing microorganisms (see, for example, Hsu, T.-A., 1996,
Pretreatment of
biomass, in Handbook on Bioethanol: Production and Utilization, Wyman, C. E.,
ed., Taylor
& Francis, Washington, DC, 179-212; Ghosh and Singh, 1993, Physicochemical and
biological treatments for enzymatic/microbial conversion of cellulosic
biomass, Adv. Appl.
Microbiol. 39: 295-333; McMillan, J. D., 1994, Pretreating lignocellulosic
biomass: a review,
in Enzymatic Conversion of Biomass for Fuels Production, Himmel, M. E., Baker,
J. 0., and
Overend, R. P., eds., ACS Symposium Series 566, American Chemical Society,
Washington, DC, chapter 15; Gong, C. S., Cao, N. J., Du, J., and Tsao, G. T.,
1999, Ethanol
production from renewable resources, in Advances in Biochemical
Engineering/Biotechnology, Scheper, T., ed., Springer-Verlag Berlin
Heidelberg, Germany,
65: 207-241; Olsson and Hahn-Hagerdal, 1996, Fermentation of lignocellulosic
hydrolysates
for ethanol production, Enz. Microb. Tech. 18: 312-331; and Vallander and
Eriksson, 1990,
Production of ethanol from lignocellulosic materials: State of the art, Adv.
Biochem.
Eng./Biotechnol. 42: 63-95).
Saccharification. In the hydrolysis step, also known as saccharification, the
cellulosic
material, e.g., pretreated, is hydrolyzed to break down cellulose and
alternatively also
hemicellulose to fermentable sugars, such as glucose, cellobiose, xylose,
xylulose,
arabinose, mannose, galactose, and/or soluble oligosaccharides. The hydrolysis
is performed
-42-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
enzymatically by an enzyme composition in the presence of a polypeptide having
cellobiohydrolase activity. The enzyme and protein components of the
compositions can be
added sequentially.
Enzymatic hydrolysis is preferably carried out in a suitable aqueous
environment under
conditions that can be readily determined by one skilled in the art. In a
preferred aspect,
hydrolysis is performed under conditions suitable for the activity of the
enzyme(s), i.e., optimal
for the enzyme(s). The hydrolysis can be carried out as a fed batch or
continuous process
where the pretreated cellulosic material (substrate) is fed gradually to, for
example, an enzyme
containing hydrolysis solution.
The saccharification is generally performed in stirred-tank reactors or
fermentors
under controlled pH, temperature, and mixing conditions. Suitable process
time, temperature
and pH conditions can readily be determined by one skilled in the art. For
example, the
saccharification can last up to 200 hours, but is typically performed for
preferably about 12 to
about 96 hours, more preferably about 16 to about 72 hours, and most
preferably about 24 to
about 48 hours. The temperature is in the range of preferably about 25 C to
about 70 C,
more preferably about 30 C to about 65 C, and more preferably about 40 C to 60
C, in
particular about 50 C. The pH is in the range of preferably about 3 to about
8, more
preferably about 3.5 to about 7, and most preferably about 4 to about 6, in
particular about
pH 5. The dry solids content is in the range of preferably about 5 to about 50
wt %, more
preferably about 10 to about 40 wt %, and most preferably about 20 to about 30
wt %.
The optimum amounts of the enzymes and polypeptides having cellobiohydrolase
activity depend on several factors including, but not limited to, the mixture
of component
cellulolytic enzymes, the cellulosic substrate, the concentration of
cellulosic substrate, the
pretreatment(s) of the cellulosic substrate, temperature, time, pH, and
inclusion of
fermenting organism (e.g., yeast for Simultaneous Saccharification and
Fermentation).
In one aspect, an effective amount of cellulolytic or hemicellulolytic enzyme
protein to
cellulosic material is about 0.5 to about 50 mg, preferably at about 0.5 to
about 40 mg, more
preferably at about 0.5 to about 25 mg, more preferably at about 0.75 to about
20 mg, more
preferably at about 0.75 to about 15 mg, even more preferably at about 0.5 to
about 10 mg,
and most preferably at about 2.5 to about 10 mg per g of cellulosic material.
In another aspect, an effective amount of a polypeptide having
cellobiohydrolase
activity to cellulosic material is about 0.01 to about 50.0 mg, preferably
about 0.01 to about
mg, more preferably about 0.01 to about 30 mg, more preferably about 0.01 to
about 20
mg, more preferably about 0.01 to about 10 mg, more preferably about 0.01 to
about 5 mg,
35 more preferably at about 0.025 to about 1.5 mg, more preferably at about
0.05 to about 1.25
mg, more preferably at about 0.075 to about 1.25 mg, more preferably at about
0.1 to about
1.25 mg, even more preferably at about 0.15 to about 1.25 mg, and most
preferably at about
-43-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
0.25 to about 1.0 mg per g of cellulosic material.
In another aspect, an effective amount of a polypeptide having
cellobiohydrolase
activity to cellulolytic enzyme protein is about 0.005 to about 1.0 g,
preferably at about 0.01
to about 1.0 g, more preferably at about 0.15 to about 0.75 g, more preferably
at about 0.15
to about 0.5 g, more preferably at about 0.1 to about 0.5 g, even more
preferably at about
0.1 to about 0.5 g, and most preferably at about 0.05 to about 0.2 g per g of
cellulolytic
enzyme protein.
The enzyme compositions can comprise any protein that is useful in degrading
or
converting a cellulosic material.
In one aspect, the enzyme composition comprises or further comprises one or
more
(several) proteins selected from the group consisting of a cellulase, a GH61
polypeptide
having cellulolytic enhancing activity, a hemicellulase, an expansin, an
esterase, a laccase,
a ligninolytic enzyme, a pectinase, a peroxidase, a protease, and a swollenin.
In another
aspect, the cellulase is preferably one or more (several) enzymes selected
from the group
consisting of an endoglucanase, a cellobiohydrolase, and a beta-glucosidase.
In another
aspect, the hemicellulase is preferably one or more (several) enzymes selected
from the
group consisting of an acetylmannan esterase, an acetyxylan esterase, an
arabinanase, an
arabinofuranosidase, a coumaric acid esterase, a feruloyl esterase, a
galactosidase, a
glucuronidase, a glucuronoyl esterase, a mannanase, a mannosidase, a xylanase,
and a
xylosidase.
In another aspect, the enzyme composition comprises one or more (several)
cellulolytic enzymes. In another aspect, the enzyme composition comprises or
further
comprises one or more (several) hemicellulolytic enzymes. In another aspect,
the enzyme
composition comprises one or more (several) cellulolytic enzymes and one or
more (several)
hemicellulolytic enzymes. In another aspect, the enzyme composition comprises
one or
more (several) enzymes selected from the group of cellulolytic enzymes and
hemicellulolytic
enzymes. In another aspect, the enzyme composition comprises an endoglucanase.
In
another aspect, the enzyme composition comprises a cellobiohydrolase. In
another aspect,
the enzyme composition comprises a beta-glucosidase. In another aspect, the
enzyme
composition comprises a polypeptide having cellulolytic enhancing activity. In
another
aspect, the enzyme composition comprises an endoglucanase and a polypeptide
having
cellulolytic enhancing activity. In another aspect, the enzyme composition
comprises a
cellobiohydrolase and a polypeptide having cellulolytic enhancing activity. In
another aspect,
the enzyme composition comprises a beta-glucosidase and a polypeptide having
cellulolytic
enhancing activity. In another aspect, the enzyme composition comprises an
endoglucanase
and a cellobiohydrolase. In another aspect, the enzyme composition comprises
an
endoglucanase and a beta-glucosidase. In another aspect, the enzyme
composition
-44-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
comprises a cellobiohydrolase and a beta-glucosidase. In another aspect, the
enzyme
composition comprises an endoglucanase, a cellobiohydrolase, and a polypeptide
having
cellulolytic enhancing activity. In another aspect, the enzyme composition
comprises an
endoglucanase, a beta-glucosidase, and a polypeptide having cellulolytic
enhancing activity.
In another aspect, the enzyme composition comprises a cellobiohydrolase, a
beta-
glucosidase, and a polypeptide having cellulolytic enhancing activity. In
another aspect, the
enzyme composition comprises an endoglucanase, a cellobiohydrolase, and a beta-
glucosidase, and a polypeptide having cellulolytic enhancing activity.
In another aspect, the enzyme composition comprises an acetylmannan esterase.
In
another aspect, the enzyme composition comprises an acetyxylan esterase. In
another
aspect, the enzyme composition comprises an arabinanase (e.g., alpha-L-
arabinanase). In
another aspect, the enzyme composition comprises an arabinofuranosidase (e.g.,
alpha-L-
arabinofuranosidase). In another aspect, the enzyme composition comprises a
coumaric
acid esterase. In another aspect, the enzyme composition comprises a feruloyl
esterase. In
another aspect, the enzyme composition comprises a galactosidase (e.g., alpha-
galactosidase and/or beta-galactosidase). In another aspect, the enzyme
composition
comprises a glucuronidase (e.g., alpha-D-glucuronidase). In another aspect,
the enzyme
composition comprises a glucuronoyl esterase. In another aspect, the enzyme
composition
comprises a mannanase. In another aspect, the enzyme composition comprises a
mannosidase (e.g., beta-mannosidase). In another aspect, the enzyme
composition
comprises a xylanase. In a preferred aspect, the xylanase is a Family 10
xylanase. In
another aspect, the enzyme composition comprises a xylosidase. In another
aspect, the
enzyme composition comprises an expansin. In another aspect, the enzyme
composition
comprises an esterase. In another aspect, the enzyme composition comprises a
laccase. In
another aspect, the enzyme composition comprises a ligninolytic enzyme. In a
preferred
aspect, the ligninolytic enzyme is a manganese peroxidase. In another
preferred aspect, the
ligninolytic enzyme is a lignin peroxidase. In another preferred aspect, the
ligninolytic
enzyme is a H202-producing enzyme. In another aspect, the enzyme composition
comprises
a pectinase. In another aspect, the enzyme composition comprises a peroxidase.
In another
aspect, the enzyme composition comprises a protease. In another aspect, the
enzyme
composition comprises a swollenin.
In the methods of the present invention, the enzyme(s) can be added prior to
or
during fermentation, e.g., during saccharification or during or after
propagation of the
fermenting microorganism(s).
One or more (several) components of the enzyme composition may be wild-type
proteins, recombinant proteins, or a combination of wild-type proteins and
recombinant
proteins. For example, one or more (several) components may be native proteins
of a cell,
-45-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
which is used as a host cell to express recombinantly one or more (several)
other
components of the enzyme composition. One or more (several) components of the
enzyme
composition may be produced as monocomponents, which are then combined to form
the
enzyme composition. The enzyme composition may be a combination of
multicomponent
and monocomponent protein preparations.
The enzymes used in the methods of the present invention may be in any form
suitable for use, such as, for example, a crude fermentation broth with or
without cells
removed, a cell lysate with or without cellular debris, a semi-purified or
purified enzyme
preparation, or a host cell as a source of the enzymes. The enzyme composition
may be a
dry powder or granulate, a non-dusting granulate, a liquid, a stabilized
liquid, or a stabilized
protected enzyme. Liquid enzyme preparations may, for instance, be stabilized
by adding
stabilizers such as a sugar, a sugar alcohol or another polyol, and/or lactic
acid or another
organic acid according to established processes.
The enzymes can be derived or obtained from any suitable origin, including,
bacterial, fungal, yeast, plant, or mammalian origin. The term "obtained"
means herein that
the enzyme may have been isolated from an organism that naturally produces the
enzyme
as a native enzyme. The term "obtained" also means herein that the enzyme may
have been
produced recombinantly in a host organism employing methods described herein,
wherein
the recombinantly produced enzyme is either native or foreign to the host
organism or has a
modified amino acid sequence, e.g., having one or more (several) amino acids
that are
deleted, inserted and/or substituted, i.e., a recombinantly produced enzyme
that is a mutant
and/or a fragment of a native amino acid sequence or an enzyme produced by
nucleic acid
shuffling processes known in the art. Encompassed within the meaning of a
native enzyme
are natural variants and within the meaning of a foreign enzyme are variants
obtained
recombinantly, such as by site-directed mutagenesis or shuffling.
The polypeptide having enzyme activity may be a bacterial polypeptide. For
example,
the polypeptide may be a gram positive bacterial polypeptide such as a
Bacillus,
Streptococcus, Streptomyces, Staphylococcus, Enterococcus, Lactobacillus,
Lactococcus,
Clostridium, Geobacillus, or Oceanobacillus polypeptide having enzyme
activity, or a Gram
negative bacterial polypeptide such as an E. coli, Pseudomonas, Salmonella,
Campylobacter, Helicobacter, Flavobacterium, Fusobacterium, llyobacter,
Neisseria, or
Ureaplasma polypeptide having enzyme activity.
In a preferred aspect, the polypeptide is a Bacillus alkalophilus, Bacillus
amyloliquefaciens, Bacillus brevis, Bacillus circulans, Bacillus clausii,
Bacillus coagulans,
Bacillus firmus, Bacillus lautus, Bacillus lentus, Bacillus licheniformis,
Bacillus megaterium,
Bacillus pumilus, Bacillus stearothermophilus, Bacillus subtilis, or Bacillus
thuringiensis
polypeptide having enzyme activity.
-46-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
In another preferred aspect, the polypeptide is a Streptococcus equisimilis,
Streptococcus pyogenes, Streptococcus uberis, or Streptococcus equi subsp.
Zooepidemicus polypeptide having enzyme activity.
In another preferred aspect, the polypeptide is a Streptomyces achromogenes,
Streptomyces avermitilis, Streptomyces coelicolor, Streptomyces griseus, or
Streptomyces
lividans polypeptide having enzyme activity.
The polypeptide having enzyme activity may also be a fungal polypeptide, and
more
preferably a yeast polypeptide such as a Candida, Kluyveromyces, Pichia,
Saccharomyces,
Schizosaccharomyces, or Yarrowia polypeptide having enzyme activity; or more
preferably a
filamentous fungal polypeptide such as an Acremonium, Agaricus, Alternaria,
Aspergillus,
Aureobasidium, Botryospaeria, Ceriporiopsis, Chaetomidium, Chrysosporium,
Claviceps,
Cochliobolus, Coprinopsis, Coptotermes, Corynascus, Cryphonectria,
Cryptococcus,
Diplodia, Exidia, Filibasidium, Fusarium, Gibberella, Holomastigotoides,
Humicola, Irpex,
Lentinula, Leptospaeria, Magnaporthe, Melanocarpus, Meripilus, Mucor,
Myceliophthora,
Neocallimastix, Neurospora, Paecilomyces, Penicillium, Phanerochaete,
Piromyces,
Poitrasia, Pseudoplectania, Pseudotrichonympha, Rhizomucor, Schizophyllum,
Scytalidium,
Talaromyces, Thermoascus, Thielavia, Tolypocladium, Trichoderma, Trichophaea,
Verticillium, Volvariella, or Xylaria polypeptide having enzyme activity.
In a preferred aspect, the polypeptide is a Saccharomyces carlsbergensis,
Saccharomyces cerevisiae, Saccharomyces diastaticus, Saccharomyces douglasii,
Saccharomyces kluyveri, Saccharomyces norbensis, or Saccharomyces oviformis
polypeptide having enzyme activity.
In another preferred aspect, the polypeptide is an Acremonium cellulolyticus,
Aspergillus aculeatus, Aspergillus awamori, Aspergillus fumigatus, Aspergillus
foetidus,
Aspergillus japonicus, Aspergillus nidulans, Aspergillus niger, Aspergillus
oryzae,
Chrysosporium keratinophilum, Chrysosporium lucknowense, Chrysosporium
tropicum,
Chrysosporium merdarium, Chrysosporium inops, Chrysosporium pannicola,
Chrysosporium
queenslandicum, Chrysosporium zonatum, Fusarium bactridioides, Fusarium
cerealis,
Fusarium crookwellense, Fusarium culmorum, Fusarium graminearum, Fusarium
graminum,
Fusarium heterosporum, Fusarium negundi, Fusarium oxysporum, Fusarium
reticulatum,
Fusarium roseum, Fusarium sambucinum, Fusarium sarcochroum, Fusarium
sporotrichioides, Fusarium sulphureum, Fusarium torulosum, Fusarium
trichothecioides,
Fusarium venenatum, Humicola grisea, Humicola insolens, Humicola lanuginosa,
Irpex
lacteus, Mucor miehei, Myceliophthora thermophila, Neurospora crassa,
Penicillium
funiculosum, Penicillium purpurogenum, Phanerochaete chrysosporium, Thielavia
achromatica, Thielavia albomyces, Thielavia albopilosa, Thielavia
australeinsis, Thielavia
fimeti, Thielavia microspora, Thielavia ovispora, Thielavia peruviana,
Thielavia
-47-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
spededonium, Thielavia setosa, Thielavia subthermophila, Thielavia terrestris,
Trichoderma
harzianum, Trichoderma koningii, Trichoderma longibrachiatum, Trichoderma
reesei,
Trichoderma viride, or Trichophaea saccata polypeptide having enzyme activity.
Chemically modified or protein engineered mutants of the polypeptides having
enzyme activity may also be used.
One or more (several) components of the enzyme composition may be a
recombinant component, i.e., produced by cloning of a DNA sequence encoding
the single
component and subsequent cell transformed with the DNA sequence and expressed
in a
host (see, for example, WO 91/17243 and WO 91/17244). The host is preferably a
heterologous host (enzyme is foreign to host), but the host may under certain
conditions also
be a homologous host (enzyme is native to host). Monocomponent cellulolytic
enzymes may
also be prepared by purifying such a protein from a fermentation broth.
In one aspect, the one or more (several) cellulolytic enzymes comprise a
commercial
cellulolytic enzyme preparation. Examples of commercial cellulolytic enzyme
preparations
suitable for use in the present invention include, for example, CELLICTM CTec
(Novozymes
A/S), CELLICTM CTec2 (Novozymes A/S), CELLUCLASTTM (Novozymes A/S), NOVOZYMTM
188 (Novozymes A/S), CELLUZYMETM (Novozymes A/S), CEREFLOTM (Novozymes A/S),
and ULTRAFLOTM (Novozymes A/S), ACCELERASETM (Genencor Int.), LAMINEXTM
(Genencor Int.), SPEZYMETM CP (Genencor Int.), ROHAMENTTM 7069 W (Rohm GmbH),
FIBREZYME LDI (Dyadic International, Inc.), FIBREZYME LBR (Dyadic
International,
Inc.), or VISCOSTAR 150L (Dyadic International, Inc.). The cellulase enzymes
are added
in amounts effective from about 0.001 to about 5.0 wt % of solids, more
preferably from
about 0.025 to about 4.0 wt % of solids, and most preferably from about 0.005
to about 2.0
wt % of solids.
Examples of bacterial endoglucanases that can be used in the methods of the
present invention, include, but are not limited to, an Acidothermus
cellulolyticus
endoglucanase (WO 91/05039; WO 93/15186; U.S. Patent No. 5,275,944; WO
96/02551;
U.S. Patent No. 5,536,655, WO 00/70031, WO 05/093050); Thermobifida fusca
endoglucanase III (WO 05/093050); and Thermobifida fusca endoglucanase V (WO
05/093050).
Examples of fungal endoglucanases that can be used in the present invention
include, but are not limited to, a Trichoderma reesei endoglucanase I
(Penttila et al., 1986,
Gene 45: 253-263; Trichoderma reesei Ce17B endoglucanase I; GENBANKTM
accession no.
M15665; SEQ ID NO: 4); Trichoderma reesei endoglucanase II (Saloheimo, et al.,
1988,
Gene 63:11-22; Trichoderma reesei Ce15A endoglucanase II; GENBANKTM accession
no.
M19373; SEQ ID NO: 6); Trichoderma reesei endoglucanase III (Okada et al.,
1988, Appl.
-48-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
Environ. Microbiol. 64: 555-563; GENBANKTM accession no. AB003694; SEQ ID NO:
8);
Trichoderma reesei endoglucanase V (Saloheimo et al., 1994, Molecular
Microbiology 13:
219-228; GENBANKTM accession no. Z33381; SEQ ID NO: 10); Aspergillus aculeatus
endoglucanase (Ooi et al., 1990, Nucleic Acids Research 18: 5884); Aspergillus
kawachii
endoglucanase (Sakamoto et al., 1995, Current Genetics 27: 435-439); Erwinia
carotovara
endoglucanase (Saarilahti et al., 1990, Gene 90: 9-14); Fusarium oxysporum
endoglucanase
(GENBANKTM accession no. L29381); Humicola grisea var. thermoidea
endoglucanase
(GENBANKTM accession no. AB003107); Melanocarpus albomyces endoglucanase
(GENBANKTM accession no. MAL515703); Neurospora crassa endoglucanase
(GENBANKTM
accession no. XM_324477); Humicola insolens endoglucanase V (SEQ ID NO: 12);
Myceliophthora thermophila CBS 117.65 endoglucanase (SEQ ID NO: 14);
basidiomycete
CBS 495.95 endoglucanase (SEQ ID NO: 16); basidiomycete CBS 494.95
endoglucanase
(SEQ ID NO: 18); Thielavia terrestris NRRL 8126 CEL6B endoglucanase (SEQ ID
NO: 20);
Thielavia terrestris NRRL 8126 CEL6C endoglucanase (SEQ ID NO: 22); Thielavia
terrestris
NRRL 8126 CEL7C endoglucanase (SEQ ID NO: 24); Thielavia terrestris NRRL 8126
CEL7E endoglucanase (SEQ ID NO: 26); Thielavia terrestris NRRL 8126 CEL7F
endoglucanase (SEQ ID NO: 28); Cladorrhinum foecundissimum ATCC 62373 CEL7A
endoglucanase (SEQ ID NO: 30); and Trichoderma reesei strain No. VTT-D-80133
endoglucanase (SEQ ID NO: 32; GENBANKTM accession no. M15665). The
endoglucanases
of SEQ ID NO: 4, SEQ ID NO: 6, SEQ ID NO: 8, SEQ ID NO: 10, SEQ ID NO: 12, SEQ
ID
NO: 14, SEQ ID NO: 16, SEQ ID NO: 18, SEQ ID NO: 20, SEQ ID NO: 22, SEQ ID NO:
24,
SEQ ID NO: 26, SEQ ID NO: 28, SEQ ID NO: 30, and SEQ ID NO: 32, described
above are
encoded by the mature polypeptide coding sequence of SEQ ID NO: 3, SEQ ID NO:
5, SEQ
ID NO: 7, SEQ ID NO: 9, SEQ ID NO: 11, SEQ ID NO: 13, SEQ ID NO: 15, SEQ ID
NO: 17,
SEQ ID NO: 19, SEQ ID NO: 21, SEQ ID NO: 23, SEQ ID NO: 25, SEQ ID NO: 27, SEQ
ID
NO: 29, and SEQ I D NO: 31, respectively.
Examples of cellobiohydrolases useful in the present invention include, but
are not
limited to, Trichoderma reesei cellobiohydrolase I (SEQ ID NO: 34);
Trichoderma reesei
cellobiohydrolase II (SEQ ID NO: 36); Humicola insolens cellobiohydrolase I
(SEQ ID NO:
38); Myceliophthora thermophila cellobiohydrolase II (SEQ ID NO: 40 and SEQ ID
NO: 42);
Thielavia terrestris cellobiohydrolase II (CEL6A) (SEQ ID NO: 44); Chaetomium
thermophilum cellobiohydrolase I (SEQ ID NO: 46); and Chaetomium thermophilum
cellobiohydrolase II (SEQ ID NO: 48), Aspergillus fumigatus cellobiohydrolase
I (SEQ ID NO:
50), and Aspergillus fumigatus cellobiohydrolase II (SEQ ID NO: 52). The
cellobiohydrolases
of SEQ ID NO: 34, SEQ ID NO: 36, SEQ ID NO: 38, SEQ ID NO: 40, SEQ ID NO: 42,
SEQ
ID NO: 44, SEQ ID NO: 46, SEQ ID NO: 48, SEQ ID NO: 50, and SEQ ID NO: 52,
described
-49-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
above are encoded by the mature polypeptide coding sequence of SEQ ID NO: 33,
SEQ ID
NO: 35, SEQ ID NO: 37, SEQ ID NO: 39, SEQ ID NO: 41, SEQ ID NO: 43, SEQ ID NO:
45,
SEQ ID NO: 47, SEQ ID NO: 49, and SEQ ID NO: 51, respectively.
Examples of beta-glucosidases useful in the present invention include, but are
not
limited to, Aspergillus oryzae beta-glucosidase (SEQ ID NO: 54); Aspergillus
fumigatus beta-
glucosidase (SEQ ID NO: 56); Penicillium brasilianum IBT 20888 beta-
glucosidase (SEQ ID
NO: 58); Aspergillus niger beta-glucosidase (SEQ ID NO: 60); and Aspergillus
aculeatus
beta-glucosidase (SEQ ID NO: 62). The beta-glucosidases of SEQ ID NO: 54, SEQ
ID NO:
56, SEQ ID NO: 58, SEQ ID NO: 60, and SEQ ID NO: 62, described above are
encoded by
the mature polypeptide coding sequence of SEQ ID NO: 53, SEQ ID NO: 55, SEQ ID
NO:
57, SEQ ID NO: 59, and SEQ ID NO: 61, respectively.
Examples of other beta-glucosidases useful in the present invention include a
Aspergillus oryzae beta-glucosidase variant fusion protein of SEQ ID NO: 64 or
the
Aspergillus oryzae beta-glucosidase fusion protein of SEQ ID NO: 66. The beta-
glucosidase
fusion proteins of SEQ ID NO: 64 and SEQ ID NO: 66 are encoded by SEQ ID NO:
63 and
SEQ ID NO: 65, respectively.
The Aspergillus oryzae beta-glucosidase can be obtained according to WO
2002/095014. The Aspergillus fumigatus beta-glucosidase can be obtained
according to WO
2005/047499. The Penicillium brasilianum beta-glucosidase can be obtained
according to
WO 2007/019442. The Aspergillus niger beta-glucosidase can be obtained
according to Dan
et al., 2000, J. Biol. Chem. 275: 4973-4980. The Aspergillus aculeatus beta-
glucosidase can
be obtained according to Kawaguchi et al., 1996, Gene 173: 287-288.
Other useful endoglucanases, cellobiohydrolases, and beta-glucosidases are
disclosed in numerous Glycosyl Hydrolase families using the classification
according to
Henrissat B., 1991, A classification of glycosyl hydrolases based on amino-
acid sequence
similarities, Biochem. J. 280: 309-316, and Henrissat B., and Bairoch A.,
1996, Updating the
sequence-based classification of glycosyl hydrolases, Biochem. J. 316: 695-
696.
Other cellulolytic enzymes that may be useful in the present invention are
described
in EP 495,257, EP 531,315, EP 531,372, WO 89/09259, WO 94/07998, WO 95/24471,
WO
96/11262, WO 96/29397, WO 96/034108, WO 97/14804, WO 98/08940, WO 98/012307,
WO 98/13465, WO 98/015619, WO 98/015633, WO 98/028411, WO 99/06574, WO
99/10481, WO 99/025846, WO 99/025847, WO 99/031255, WO 2000/009707, WO
2002/050245, WO 2002/0076792, WO 2002/101078, WO 2003/027306, WO 2003/052054,
WO 2003/052055, WO 2003/052056, WO 2003/052057, WO 2003/052118, WO
2004/016760, WO 2004/043980, WO 2004/048592, WO 2005/001065, WO 2005/028636,
WO 2005/093050, WO 2005/093073, WO 2006/074005, WO 2006/117432, WO
2007/071818, WO 2007/071820, WO 2008/008070, WO 2008/008793, U.S. Patent No.
-50-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
4,435,307, U.S. Patent No. 5,457,046, U.S. Patent No. 5,648,263, U.S. Patent
No.
5,686,593, U.S. Patent No. 5,691,178, U.S. Patent No. 5,763,254, and U.S.
Patent No.
5,776,757.
In the methods of the present invention, any GH61 polypeptide having
cellulolytic
enhancing activity can be used.
In a first aspect, the polypeptide having cellulolytic enhancing activity
comprises the
following motifs:
[ILMV]-P-X(4,5)-G-X-Y-[ILMV]-X-R-X-[EQ]-X(4)-[HNQ] and [FW]-[TF]-K-[AIV],
wherein X is any amino acid, X(4,5) is any amino acid at 4 or 5 contiguous
positions,
and X(4) is any amino acid at 4 contiguous positions.
The polypeptide comprising the above-noted motifs may further comprise:
H-X(1,2)-G-P-X(3)-[YW]-[Al LMV],
[EQ]-X-Y-X(2)-C-X-[EHQN]-[FILV]-X-[ILV], or
H-X(1,2)-G-P-X(3)-[YW]-[AILMV] and [EQ]-X-Y-X(2)-C-X-[EHQN]-[FILV]-X-[ILV],
wherein X is any amino acid, X(1,2) is any amino acid at 1 position or 2
contiguous
positions, X(3) is any amino acid at 3 contiguous positions, and X(2) is any
amino acid at 2
contiguous positions. In the above motifs, the accepted IUPAC single letter
amino acid
abbreviation is employed.
In a preferred aspect, the polypeptide having cellulolytic enhancing activity
further
comprises H-X(1,2)-G-P-X(3)-[YW]-[AILMV]. In another preferred aspect, the
isolated
polypeptide having cellulolytic enhancing activity further comprises [EQ]-X-Y-
X(2)-C-X-
[EHQN]-[FILV]-X-[ILV]. In another preferred aspect, the polypeptide having
cellulolytic
enhancing activity further comprises H-X(1,2)-G-P-X(3)-[YW]-[AILMV] and [EQ]-X-
Y-X(2)-C-
X-[EHQN]-[FI LV]-X-[I LV].
In a second aspect, the polypeptide having cellulolytic enhancing activity
comprises
the following motif:
[I LMV]-P-x(4,5)-G-x-Y-[I LMV]-x-R-x-[EQ]-x(3)-A-[H NQ],
wherein x is any amino acid, x(4,5) is any amino acid at 4 or 5 contiguous
positions,
and x(3) is any amino acid at 3 contiguous positions. In the above motif, the
accepted
IUPAC single letter amino acid abbreviation is employed.
In a third aspect, the polypeptide having cellulolytic enhancing activity
comprises an
amino acid sequence that has a degree of identity to the mature polypeptide of
SEQ ID NO:
68, SEQ ID NO: 70, SEQ ID NO: 72, SEQ ID NO: 74, SEQ ID NO: 76, SEQ ID NO: 78,
SEQ
ID NO: 80, SEQ ID NO: 82, SEQ ID NO: 84, SEQ ID NO: 86, SEQ ID NO: 88, SEQ ID
NO:
90, SEQ ID NO: 92, SEQ ID NO: 94, SEQ ID NO: 96, SEQ ID NO: 98, SEQ ID NO:
100,
SEQ ID NO: 102, SEQ ID NO: 104, SEQ ID NO: 106, SEQ ID NO: 108, SEQ ID NO:
110,
SEQ ID NO: 112, SEQ ID NO: 114, SEQ ID NO: 116, SEQ ID NO: 118, SEQ ID NO:
120,
-51-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
SEQ ID NO: 122, SEQ ID NO: 124, SEQ ID NO: 126, SEQ ID NO: 128, or SEQ ID NO:
130
of at least 60%, e.g., at least 65%, at least 70%, at least 75%, at least 80%,
at least 85%, at
least 90%, at least 91 %, at least 92%, at least 93%, at least 94%, or at
least 95%, at least
96%, at least 97%, at least 98%, at least 99%, or at least 100%.
In a fourth aspect, the polypeptide having cellulolytic enhancing activity is
encoded
by a polynucleotide that hybridizes under at least very low stringency
conditions, preferably
at least low stringency conditions, more preferably at least medium stringency
conditions,
more preferably at least medium-high stringency conditions, even more
preferably at least
high stringency conditions, and most preferably at least very high stringency
conditions with
(i) the mature polypeptide coding sequence of SEQ ID NO: 67, SEQ ID NO: 69,
SEQ ID NO:
71, SEQ ID NO: 73, SEQ ID NO: 75, SEQ ID NO: 77, SEQ ID NO: 79, SEQ ID NO: 81,
SEQ
ID NO: 83, SEQ ID NO: 85, SEQ ID NO: 87, SEQ ID NO: 89, SEQ ID NO: 91, SEQ ID
NO:
93, SEQ ID NO: 95, SEQ ID NO: 97, SEQ ID NO: 99, SEQ ID NO: 101, SEQ ID NO:
103,
SEQ ID NO: 105, SEQ ID NO: 107, SEQ ID NO: 109, SEQ ID NO: 111, SEQ ID NO:
113,
SEQ ID NO: 115, SEQ ID NO: 117, SEQ ID NO: 119, SEQ ID NO: 121, SEQ ID NO:
123,
SEQ ID NO: 125, SEQ ID NO: 127, or SEQ ID NO: 129, (ii) the cDNA sequence
contained in
the mature polypeptide coding sequence of SEQ ID NO: 73, SEQ ID NO: 75, SEQ ID
NO:
77, or SEQ ID NO: 81, or the genomic DNA sequence comprising the mature
polypeptide
coding sequence of SEQ ID NO: 67, SEQ ID NO: 69, SEQ ID NO: 71, SEQ ID NO: 79,
SEQ
ID NO: 83, SEQ ID NO: 85, SEQ ID NO: 87, SEQ ID NO: 89, SEQ ID NO: 91, SEQ ID
NO:
93, SEQ ID NO: 95, SEQ ID NO: 97, SEQ ID NO: 99, SEQ ID NO: 101, SEQ ID NO:
103,
SEQ ID NO: 105, SEQ ID NO: 107, SEQ ID NO: 109, SEQ ID NO: 111, SEQ ID NO:
113,
SEQ ID NO: 115, SEQ ID NO: 117, SEQ ID NO: 119, SEQ ID NO: 121, SEQ ID NO:
123,
SEQ ID NO: 125, SEQ ID NO: 127, or SEQ ID NO: 129, (iii) a subsequence of (i)
or (ii), or
(iv) a full-length complementary strand of (i), (ii), or (iii) (J. Sambrook,
E.F. Fritsch, and T.
Maniatus, 1989, supra). A subsequence of the mature polypeptide coding
sequence of SEQ
ID NO: 67, SEQ ID NO: 69, SEQ ID NO: 71, SEQ ID NO: 73, SEQ ID NO: 75, SEQ ID
NO:
77, SEQ ID NO: 79, SEQ ID NO: 81, SEQ ID NO: 83, SEQ ID NO: 85, SEQ ID NO: 87,
SEQ
ID NO: 89, SEQ ID NO: 91, SEQ ID NO: 93, SEQ ID NO: 95, SEQ ID NO: 97, SEQ ID
NO:
99, SEQ ID NO: 101, SEQ ID NO: 103, SEQ ID NO: 105, SEQ ID NO: 107, SEQ ID NO:
109, SEQ ID NO: 111, SEQ ID NO: 113, SEQ ID NO: 115, SEQ ID NO: 117, SEQ ID
NO:
119, SEQ ID NO: 121, SEQ ID NO: 123, SEQ ID NO: 125, SEQ ID NO: 127, or SEQ ID
NO:
129 contains at least 100 contiguous nucleotides or preferably at least 200
contiguous
nucleotides. Moreover, the subsequence may encode a polypeptide fragment that
has
cellulolytic enhancing activity.
In a fifth aspect, the polypeptide having cellulolytic enhancing activity is
encoded by a
polynucleotide comprising or consisting of a nucleotide sequence that has a
degree of
-52-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
identity to the mature polypeptide coding sequence of SEQ ID NO: 67, SEQ ID
NO: 69, SEQ
ID NO: 71, SEQ ID NO: 73, SEQ ID NO: 75, SEQ ID NO: 77, SEQ ID NO: 79, SEQ ID
NO:
81, SEQ ID NO: 83, SEQ ID NO: 85, SEQ ID NO: 87, SEQ ID NO: 89, SEQ ID NO: 91,
SEQ
ID NO: 93, SEQ ID NO: 95, SEQ ID NO: 97, SEQ ID NO: 99, SEQ ID NO: 101, SEQ ID
NO:
103, SEQ ID NO: 105, SEQ ID NO: 107, SEQ ID NO: 109, SEQ ID NO: 111, SEQ ID
NO:
113, SEQ ID NO: 115, SEQ ID NO: 117, SEQ ID NO: 119, SEQ ID NO: 121, SEQ ID
NO:
123, SEQ ID NO: 125, SEQ ID NO: 127, or SEQ ID NO: 129 of preferably at least
60%,
more preferably at least 65%, more preferably at least 70%, more preferably at
least 75%,
more preferably at least 80%, more preferably at least 85%, even more
preferably at least
90%, most preferably at least 91 %, at least 92%, at least 93%, at least 94%,
or at least 95%,
and even most preferably at least 96%, at least 97%, at least 98%, at least
99%, or at least
100%.
In a sixth aspect, the polypeptide having cellulolytic enhancing activity is
an artificial
variant comprising a substitution, deletion, and/or insertion of one or more
(or several) amino
acids of the mature polypeptide of SEQ ID NO: 68, SEQ ID NO: 70, SEQ ID NO:
72, SEQ ID
NO: 74, SEQ ID NO: 76, SEQ ID NO: 78, SEQ ID NO: 80, SEQ ID NO: 82, SEQ ID NO:
84,
SEQ ID NO: 86, SEQ ID NO: 88, SEQ ID NO: 90, SEQ ID NO: 92, SEQ ID NO: 94, SEQ
ID
NO: 96, SEQ ID NO: 98, SEQ ID NO: 100, SEQ ID NO: 102, SEQ ID NO: 104, SEQ ID
NO:
106, SEQ ID NO: 108, SEQ ID NO: 110, SEQ ID NO: 112, SEQ ID NO: 114, SEQ ID
NO:
116, SEQ ID NO: 118, SEQ ID NO: 120, SEQ ID NO: 122, SEQ ID NO: 124, SEQ ID
NO:
126, SEQ ID NO: 128, or SEQ ID NO: 130; or a homologous sequence thereof.
Preferably, amino acid changes are of a minor nature, that is conservative
amino
acid substitutions or insertions that do not significantly affect the folding
and/or activity of the
protein; small deletions, typically of one to about 30 amino acids; small
amino- or carboxyl-
terminal extensions, such as an amino-terminal methionine residue; a small
linker peptide of
up to about 20-25 residues; or a small extension that facilitates purification
by changing net
charge or another function, such as a poly-histidine tract, an antigenic
epitope or a binding
domain.
Examples of conservative substitutions are within the group of basic amino
acids
(arginine, lysine and histidine), acidic amino acids (glutamic acid and
aspartic acid), polar
amino acids (glutamine and asparagine), hydrophobic amino acids (leucine,
isoleucine and
valine), aromatic amino acids (phenylalanine, tryptophan and tyrosine), and
small amino
acids (glycine, alanine, serine, threonine and methionine). Amino acid
substitutions that do
not generally alter specific activity are known in the art and are described,
for example, by H.
Neurath and R.L. Hill, 1979, In, The Proteins, Academic Press, New York. The
most
commonly occurring exchanges are Ala/Ser, Val/Ile, Asp/Glu, Thr/Ser, Ala/Gly,
Ala/Thr,
Ser/Asn, Ala/Val, Ser/Gly, Tyr/Phe, Ala/Pro, Lys/Arg, Asp/Asn, Leu/Ile,
Leu/Val, Ala/Glu, and
-53-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
Asp/Gly.
Alternatively, the amino acid changes are of such a nature that the physico-
chemical
properties of the polypeptides are altered. For example, amino acid changes
may improve
the thermal stability of the polypeptide, alter the substrate specificity,
change the pH
optimum, and the like.
Essential amino acids in a parent polypeptide can be identified according to
procedures known in the art, such as site-directed mutagenesis or alanine-
scanning
mutagenesis (Cunningham and Wells, 1989, Science 244: 1081-1085). In the
latter
technique, single alanine mutations are introduced at every residue in the
molecule, and the
resultant mutant molecules are tested for cellulolytic enhancing activity to
identify amino acid
residues that are critical to the activity of the molecule. See also, Hilton
et al., 1996, J. Biol.
Chem. 271: 4699-4708. The active site of the enzyme or other biological
interaction can also
be determined by physical analysis of structure, as determined by such
techniques as
nuclear magnetic resonance, crystallography, electron diffraction, or
photoaffinity labeling, in
conjunction with mutation of putative contact site amino acids. See, for
example, de Vos et
al., 1992, Science 255: 306-312; Smith et al., 1992, J. Mol. Biol. 224: 899-
904; Wlodaver et
al., 1992, FEBS Lett. 309: 59-64. The identities of essential amino acids can
also be inferred
from analysis of identities with polypeptides that are related to the parent
polypeptide.
Single or multiple amino acid substitutions, deletions, and/or insertions can
be made
and tested using known methods of mutagenesis, recombination, and/or
shuffling, followed
by a relevant screening procedure, such as those disclosed by Reidhaar-Olson
and Sauer,
1988, Science 241: 53-57; Bowie and Sauer, 1989, Proc. Natl. Acad. Sci. USA
86: 2152-
2156; WO 95/17413; or WO 95/22625. Other methods that can be used include
error-prone
PCR, phage display (e.g., Lowman et al., 1991, Biochemistry 30: 10832-10837;
U.S. Patent
No. 5,223,409; WO 92/06204), and region-directed mutagenesis (Derbyshire et
al., 1986,
Gene 46: 145; Ner et al., 1988, DNA 7: 127).
Mutagenesis/shuffling methods can be combined with high-throughput, automated
screening methods to detect activity of cloned, mutagenized polypeptides
expressed by host
cells (Ness et al., 1999, Nature Biotechnology 17: 893-896). Mutagenized DNA
molecules
that encode active polypeptides can be recovered from the host cells and
rapidly sequenced
using standard methods in the art. These methods allow the rapid determination
of the
importance of individual amino acid residues in a polypeptide.
The total number of amino acid substitutions, deletions and/or insertions of
the
mature polypeptide of SEQ ID NO: 68, SEQ ID NO: 70, SEQ ID NO: 72, SEQ ID NO:
74,
SEQ ID NO: 76, SEQ ID NO: 78, SEQ ID NO: 80, SEQ ID NO: 82, SEQ ID NO: 84, SEQ
ID
NO: 86, SEQ ID NO: 88, SEQ ID NO: 90, SEQ ID NO: 92, SEQ ID NO: 94, SEQ ID NO:
96,
SEQ ID NO: 98, SEQ ID NO: 100, SEQ ID NO: 102, SEQ ID NO: 104, SEQ ID NO: 106,
-54-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
SEQ ID NO: 108, SEQ ID NO: 110, SEQ ID NO: 112, SEQ ID NO: 114, SEQ ID NO:
116,
SEQ ID NO: 118, SEQ ID NO: 120, SEQ ID NO: 122, SEQ ID NO: 124, SEQ ID NO:
126,
SEQ ID NO: 128, or SEQ ID NO: 130 is not more than 4, e.g., 1, 2, 3, or 4.
In one aspect, the one or more (several) hemicellulolytic enzymes comprise a
commercial hemicellulolytic enzyme preparation. Examples of commercial
hemicellulolytic
enzyme preparations suitable for use in the present invention include, for
example,
SHEARZYMETM (Novozymes A/S), CELLICTM HTec (Novozymes A/S), CELLICTM HTec2
(Novozymes A/S), VISCOZYME (Novozymes A/S), ULTRAFLO (Novozymes A/S),
PULPZYME HC (Novozymes A/S), MULTIFECT Xylanase (Genencor), ECOPULP TX-
200A (AB Enzymes), HSP 6000 Xylanase (DSM), DEPOLTM 333P (Biocatalysts Limit,
Wales, UK), DEPOLTM 740L. (Biocatalysts Limit, Wales, UK), and DEPOLTM 762P
(Biocatalysts Limit, Wales, UK).
Examples of xylanases useful in the methods of the present invention include,
but
are not limited to, Aspergillus aculeatus xylanase (GeneSeqP:AAR63790; WO
94/21785),
Aspergillus fumigatus xylanases (WO 2006/078256; xyl 3 SEQ ID NO: 131 [DNA
sequence]
and SEQ ID NO: 132 [deduced amino acid sequence]), and Thielavia terrestris
NRRL 8126
xylanases (WO 2009/079210).
Examples of beta-xylosidases useful in the methods of the present invention
include,
but are not limited to, Trichoderma reesei beta-xylosidase (UniProtKB/TrEMBL
accession
number Q92458; SEQ ID NO: 133 [DNA sequence] and SEQ ID NO: 134 [deduced amino
acid sequence]), Talaromyces emersonii (SwissProt accession number Q8X212),
and
Neurospora crassa (SwissProt accession number Q7SOW4).
Examples of acetylxylan esterases useful in the methods of the present
invention
include, but are not limited to, Hypocrea jecorina acetylxylan esterase (WO
2005/001036),
Neurospora crassa acetylxylan esterase (UniProt accession number q7s259),
Thielavia
terrestris NRRL 8126 acetylxylan esterase (WO 2009/042846), Chaetomium
globosum
acetylxylan esterase (Uniprot accession number Q2GWX4), Chaetomium gracile
acetylxylan
esterase (GeneSeqP accession number AAB82124), Phaeosphaeria nodorum
acetylxylan
esterase (Uniprot accession number QOUHJ1), and Humicola insolens DSM 1800
acetylxylan esterase (WO 2009/073709).
Examples of ferulic acid esterases useful in the methods of the present
invention
include, but are not limited to, Humicola insolens DSM 1800 feruloyl esterase
(WO
2009/076122), Neurospora crassa feruloyl esterase (UniProt accession number
Q9HGR3),
and Neosartorya fischeri feruloyl esterase (UniProt Accession number Al D9T4).
Examples of arabinofuranosidases useful in the methods of the present
invention
include, but are not limited to, Humicola insolens DSM 1800
arabinofuranosidase (WO
2009/073383) and Aspergillus niger arabinofuranosidase (GeneSeqP accession
number
-55-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
AAR94170).
Examples of alpha-glucuronidases useful in the methods of the present
invention
include, but are not limited to, Aspergillus clavatus alpha-glucuronidase
(UniProt accession
number alccl2), Trichoderma reesei alpha-glucuronidase (Uniprot accession
number
Q99024), Talaromyces emersonii alpha-glucuronidase (UniProt accession number
Q8X21 1),
Aspergillus niger alpha-glucuronidase (Uniprot accession number Q96WX9),
Aspergillus
terreus alpha-glucuronidase (SwissProt accession number QOCJP9), and
Aspergillus
fumigatus alpha-glucuronidase (SwissProt accession number Q4WW45).
The enzymes and proteins used in the methods of the present invention may be
produced by fermentation of the above-noted microbial strains on a nutrient
medium
containing suitable carbon and nitrogen sources and inorganic salts, using
procedures
known in the art (see, e.g., Bennett, J.W. and LaSure, L. (eds.), More Gene
Manipulations in
Fungi, Academic Press, CA, 1991). Suitable media are available from commercial
suppliers
or may be prepared according to published compositions (e.g., in catalogues of
the
American Type Culture Collection). Temperature ranges and other conditions
suitable for
growth and enzyme production are known in the art (see, e.g., Bailey, J.E.,
and Ollis, D.F.,
Biochemical Engineering Fundamentals, McGraw-Hill Book Company, NY, 1986).
The fermentation can be any method of cultivation of a cell resulting in the
expression or isolation of an enzyme. Fermentation may, therefore, be
understood as
comprising shake flask cultivation, or small- or large-scale fermentation
(including
continuous, batch, fed-batch, or solid state fermentations) in laboratory or
industrial
fermentors performed in a suitable medium and under conditions allowing the
enzyme to be
expressed or isolated. The resulting enzymes produced by the methods described
above
may be recovered from the fermentation medium and purified by conventional
procedures.
Fermentation. The fermentable sugars obtained from the hydrolyzed cellulosic
material can be fermented by one or more (several) fermenting microorganisms
capable of
fermenting the sugars directly or indirectly into a desired fermentation
product.
"Fermentation" or "fermentation process" refers to any fermentation process or
any process
comprising a fermentation step. Fermentation processes also include
fermentation
processes used in the consumable alcohol industry (e.g., beer and wine), dairy
industry
(e.g., fermented dairy products), leather industry, and tobacco industry. The
fermentation
conditions depend on the desired fermentation product and fermenting organism
and can
easily be determined by one skilled in the art.
In the fermentation step, sugars, released from the cellulosic material as a
result of
the pretreatment and enzymatic hydrolysis steps, are fermented to a product,
e.g., ethanol,
by a fermenting organism, such as yeast. Hydrolysis (saccharification) and
fermentation can
be separate or simultaneous, as described herein.
-56-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
Any suitable hydrolyzed cellulosic material can be used in the fermentation
step in
practicing the present invention. The material is generally selected based on
the desired
fermentation product, i.e., the substance to be obtained from the
fermentation, and the
process employed, as is well known in the art.
The term "fermentation medium" is understood herein to refer to a medium
before the
fermenting microorganism(s) is(are) added, such as, a medium resulting from a
saccharification process, as well as a medium used in a simultaneous
saccharification and
fermentation process (SSF).
"Fermenting microorganism" refers to any microorganism, including bacterial
and
fungal organisms, suitable for use in a desired fermentation process to
produce a
fermentation product. The fermenting organism can be C6 and/or C5 fermenting
organisms, or
a combination thereof. Both C6 and C5 fermenting organisms are well known in
the art. Suitable
fermenting microorganisms are able to ferment, i.e., convert, sugars, such as
glucose,
xylose, xylulose, arabinose, maltose, mannose, galactose, or oligosaccharides,
directly or
indirectly into the desired fermentation product.
Examples of bacterial and fungal fermenting organisms producing ethanol are
described by Lin et al., 2006, Appl. Microbiol. Biotechnol. 69: 627-642.
Examples of fermenting microorganisms that can ferment C6 sugars include
bacterial
and fungal organisms, such as yeast. Preferred yeast includes strains of the
Saccharomyces
spp., preferably Saccharomyces cerevisiae.
Examples of fermenting organisms that can ferment C5 sugars include bacterial
and
fungal organisms, such as some yeast. Preferred C5 fermenting yeast include
strains of Pichia,
preferably Pichia stipitis, such as Pichia stipitis CBS 5773; strains of
Candida, preferably
Candida boidinii, Candida brassicae, Candida sheatae, Candida diddensii,
Candida
pseudotropicalis, or Candida utilis.
Other fermenting organisms include strains of Zymomonas, such as Zymomonas
mobilis; Hansenula, such as Hansenula anomala; Kluyveromyces, such as K.
fragilis;
Schizosaccharomyces, such as S. pombe; E. coli, especially E. coli strains
that have been
genetically modified to improve the yield of ethanol; Clostridium, such as
Clostridium
acetobutylicum, Chlostridium thermocellum, and Chlostridium phytofermentans;
Geobacillus
sp.; Thermoanaerobacter, such as Thermoanaerobacter saccharolyticum; and
Bacillus, such
as Bacillus coagulans.
In a preferred aspect, the yeast is a Saccharomyces spp. In a more preferred
aspect,
the yeast is Saccharomyces cerevisiae. In another more preferred aspect, the
yeast is
Saccharomyces distaticus. In another more preferred aspect, the yeast is
Saccharomyces
uvarum. In another preferred aspect, the yeast is a Kluyveromyces. In another
more
preferred aspect, the yeast is Kluyveromyces marxianus. In another more
preferred aspect,
-57-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
the yeast is Kluyveromyces fragilis. In another preferred aspect, the yeast is
a Candida. In
another more preferred aspect, the yeast is Candida boidinii. In another more
preferred
aspect, the yeast is Candida brassicae. In another more preferred aspect, the
yeast is
Candida diddensii. In another more preferred aspect, the yeast is Candida
pseudotropicalis.
In another more preferred aspect, the yeast is Candida utilis. In another
preferred aspect, the
yeast is a Clavispora. In another more preferred aspect, the yeast is
Clavispora lusitaniae. In
another more preferred aspect, the yeast is Clavispora opuntiae. In another
preferred
aspect, the yeast is a Pachysolen. In another more preferred aspect, the yeast
is
Pachysolen tannophilus. In another preferred aspect, the yeast is a Pichia. In
another more
preferred aspect, the yeast is a Pichia stipitis. In another preferred aspect,
the yeast is a
Bretannomyces. In another more preferred aspect, the yeast is Bretannomyces
clausenii
(Philippidis, G. P., 1996, Cellulose bioconversion technology, in Handbook on
Bioethanol:
Production and Utilization, Wyman, C. E., ed., Taylor & Francis, Washington,
DC, 179-212).
Bacteria that can efficiently ferment hexose and pentose to ethanol include,
for
example, Zymomonas mobilis, Clostridium acetobutylicum, Clostridium
thermocellum,
Chlostridium phytofermentans, Geobacillus sp., Thermoanaerobacter
saccharolyticum, and
Bacillus coagulans (Philippidis, 1996, supra).
In a preferred aspect, the bacterium is a Zymomonas. In a more preferred
aspect, the
bacterium is Zymomonas mobilis. In another preferred aspect, the bacterium is
a
Clostridium. In another more preferred aspect, the bacterium is Clostridium
thermocellum.
Commercially available yeast suitable for ethanol production includes, e.g.,
ETHANOL
REDTM yeast (Fermentis/Lesaffre, USA), FALITM (Fleischmann's Yeast, USA),
SUPERSTARTTM and THERMOSACCTM fresh yeast (Ethanol Technology, WI, USA),
BIOFERMTM AFT and XR (NABC - North American Bioproducts Corporation, GA, USA),
GERT
STRAND TM (Gert Strand AB, Sweden), and FERMIOLTM (DSM Specialties).
In a preferred aspect, the fermenting microorganism has been genetically
modified to
provide the ability to ferment pentose sugars, such as xylose utilizing,
arabinose utilizing,
and xylose and arabinose co-utilizing microorganisms.
The cloning of heterologous genes into various fermenting microorganisms has
led to
the construction of organisms capable of converting hexoses and pentoses to
ethanol
(cofermentation) (Chen and Ho, 1993, Cloning and improving the expression of
Pichia stipitis
xylose reductase gene in Saccharomyces cerevisiae, Appl. Biochem. Biotechnol.
39-40:
135-147; Ho et al., 1998, Genetically engineered Saccharomyces yeast capable
of
effectively cofermenting glucose and xylose, Appl. Environ. Microbiol. 64:
1852-1859; Kotter
and Ciriacy, 1993, Xylose fermentation by Saccharomyces cerevisiae, Appl.
Microbiol.
Biotechnol. 38: 776-783; Walfridsson et al., 1995, Xylose-metabolizing
Saccharomyces
cerevisiae strains overexpressing the TKL1 and TALI genes encoding the pentose
-58-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
phosphate pathway enzymes transketolase and transaldolase, Appl. Environ.
Microbiol. 61:
4184-4190; Kuyper et al., 2004, Minimal metabolic engineering of Saccharomyces
cerevisiae for efficient anaerobic xylose fermentation: a proof of principle,
FEMS Yeast
Research 4: 655-664; Beall et al., 1991, Parametric studies of ethanol
production from
xylose and other sugars by recombinant Escherichia coli, Biotech. Bioeng. 38:
296-303;
Ingram et al., 1998, Metabolic engineering of bacteria for ethanol production,
Biotechnol.
Bioeng. 58: 204-214; Zhang et al., 1995, Metabolic engineering of a pentose
metabolism
pathway in ethanologenic Zymomonas mobilis, Science 267: 240-243; Deanda et
al., 1996,
Development of an arabinose-fermenting Zymomonas mobilis strain by metabolic
pathway
engineering, Appl. Environ. Microbiol. 62: 4465-4470; WO 2003/062430, xylose
isomerase).
In a preferred aspect, the genetically modified fermenting microorganism is
Saccharomyces cerevisiae. In another preferred aspect, the genetically
modified fermenting
microorganism is Zymomonas mobilis. In another preferred aspect, the
genetically modified
fermenting microorganism is Escherichia coli. In another preferred aspect, the
genetically
modified fermenting microorganism is Klebsiella oxytoca. In another preferred
aspect, the
genetically modified fermenting microorganism is Kluyveromyces sp.
It is well known in the art that the organisms described above can also be
used to
produce other substances, as described herein.
The fermenting microorganism is typically added to the degraded lignocellulose
or
hydrolysate and the fermentation is performed for about 8 to about 96 hours,
such as about
24 to about 60 hours. The temperature is typically between about 26 C to about
60 C, in
particular about 32 C or 50 C, and at about pH 3 to about pH 8, such as around
pH 4-5, 6,
or 7.
In a preferred aspect, the yeast and/or another microorganism is applied to
the
degraded cellulosic material and the fermentation is performed for about 12 to
about 96
hours, such as typically 24-60 hours. In a preferred aspect, the temperature
is preferably
between about 20 C to about 60 C, more preferably about 25 C to about 50 C,
and most
preferably about 32 C to about 50 C, in particular about 32 C or 50 C, and the
pH is
generally from about pH 3 to about pH 7, preferably around pH 4-7. However,
some
fermenting organisms, e.g., bacteria, have higher fermentation temperature
optima. Yeast or
another microorganism is preferably applied in amounts of approximately 105 to
1012,
preferably from approximately 107 to 1010, especially approximately 2 x 10$
viable cell count
per ml of fermentation broth. Further guidance in respect of using yeast for
fermentation can
be found in, e.g., "The Alcohol Textbook" (Editors K. Jacques, T.P. Lyons and
D.R. Kelsall,
Nottingham University Press, United Kingdom 1999), which is hereby
incorporated by
reference.
For ethanol production, following the fermentation the fermented slurry is
distilled to
-59-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
extract the ethanol. The ethanol obtained according to the methods of the
invention can be
used as, e.g., fuel ethanol, drinking ethanol, i.e., potable neutral spirits,
or industrial ethanol.
A fermentation stimulator can be used in combination with any of the processes
described herein to further improve the fermentation process, and in
particular, the
performance of the fermenting microorganism, such as, rate enhancement and
ethanol yield.
A "fermentation stimulator" refers to stimulators for growth of the fermenting
microorganisms,
in particular, yeast. Preferred fermentation stimulators for growth include
vitamins and
minerals. Examples of vitamins include multivitamins, biotin, pantothenate,
nicotinic acid,
meso-inositol, thiamine, pyridoxine, para-aminobenzoic acid, folic acid,
riboflavin, and
Vitamins A, B, C, D, and E. See, for example, Alfenore et al., Improving
ethanol production
and viability of Saccharomyces cerevisiae by a vitamin feeding strategy during
fed-batch
process, Springer-Verlag (2002), which is hereby incorporated by reference.
Examples of
minerals include minerals and mineral salts that can supply nutrients
comprising P, K, Mg, S,
Ca, Fe, Zn, Mn, and Cu.
Fermentation products: A fermentation product can be any substance derived
from
the fermentation. The fermentation product can be, without limitation, an
alcohol (e.g.,
arabinitol, butanol, ethanol, glycerol, methanol, 1,3-propanediol, sorbitol,
and xylitol); an
organic acid (e.g., acetic acid, acetonic acid, adipic acid, ascorbic acid,
citric acid, 2,5-diketo-
D-gluconic acid, formic acid, fumaric acid, glucaric acid, gluconic acid,
glucuronic acid,
glutaric acid, 3-hydroxypropionic acid, itaconic acid, lactic acid, malic
acid, malonic acid,
oxalic acid, oxaloacetic acid, propionic acid, succinic acid, and xylonic
acid); a ketone (e.g.,
acetone); an amino acid (e.g., aspartic acid, glutamic acid, glycine, lysine,
serine, and
threonine); and a gas (e.g., methane, hydrogen (H2), carbon dioxide (C02), and
carbon
monoxide (CO)). The fermentation product can also be protein as a high value
product.
In a preferred aspect, the fermentation product is an alcohol. It will be
understood that
the term "alcohol" encompasses a substance that contains one or more hydroxyl
moieties. In
a more preferred aspect, the alcohol is arabinitol. In another more preferred
aspect, the
alcohol is butanol. In another more preferred aspect, the alcohol is ethanol.
In another more
preferred aspect, the alcohol is glycerol. In another more preferred aspect,
the alcohol is
methanol. In another more preferred aspect, the alcohol is 1,3-propanediol. In
another more
preferred aspect, the alcohol is sorbitol. In another more preferred aspect,
the alcohol is
xylitol. See, for example, Gong, C. S., Cao, N. J., Du, J., and Tsao, G. T.,
1999, Ethanol
production from renewable resources, in Advances in Biochemical
Engineering/Biotechnology, Scheper, T., ed., Springer-Verlag Berlin
Heidelberg, Germany,
65: 207-241; Silveira, M. M., and Jonas, R., 2002, The biotechnological
production of
sorbitol, Appl. Microbiol. Biotechnol. 59: 400-408; Nigam, P., and Singh, D.,
1995, Processes
for fermentative production of xylitol - a sugar substitute, Process
Biochemistry 30 (2): 117-
-60-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
124; Ezeji, T. C., Qureshi, N. and Blaschek, H. P., 2003, Production of
acetone, butanol and
ethanol by Clostridium beijerinckii BA101 and in situ recovery by gas
stripping, World
Journal of Microbiology and Biotechnology 19 (6): 595-603.
In another preferred aspect, the fermentation product is an organic acid. In
another
more preferred aspect, the organic acid is acetic acid. In another more
preferred aspect, the
organic acid is acetonic acid. In another more preferred aspect, the organic
acid is adipic
acid. In another more preferred aspect, the organic acid is ascorbic acid. In
another more
preferred aspect, the organic acid is citric acid. In another more preferred
aspect, the organic
acid is 2,5-diketo-D-gluconic acid. In another more preferred aspect, the
organic acid is
formic acid. In another more preferred aspect, the organic acid is fumaric
acid. In another
more preferred aspect, the organic acid is glucaric acid. In another more
preferred aspect,
the organic acid is gluconic acid. In another more preferred aspect, the
organic acid is
glucuronic acid. In another more preferred aspect, the organic acid is
glutaric acid. In
another preferred aspect, the organic acid is 3-hydroxypropionic acid. In
another more
preferred aspect, the organic acid is itaconic acid. In another more preferred
aspect, the
organic acid is lactic acid. In another more preferred aspect, the organic
acid is malic acid. In
another more preferred aspect, the organic acid is malonic acid. In another
more preferred
aspect, the organic acid is oxalic acid. In another more preferred aspect, the
organic acid is
propionic acid. In another more preferred aspect, the organic acid is succinic
acid. In another
more preferred aspect, the organic acid is xylonic acid. See, for example,
Chen, R., and Lee,
Y. Y., 1997, Membrane-mediated extractive fermentation for lactic acid
production from
cellulosic biomass, Appl. Biochem. Biotechnol. 63-65: 435-448.
In another preferred aspect, the fermentation product is a ketone. It will be
understood that the term "ketone" encompasses a substance that contains one or
more
ketone moieties. In another more preferred aspect, the ketone is acetone. See,
for example,
Qureshi and Blaschek, 2003, supra.
In another preferred aspect, the fermentation product is an amino acid. In
another
more preferred aspect, the organic acid is aspartic acid. In another more
preferred aspect,
the amino acid is glutamic acid. In another more preferred aspect, the amino
acid is glycine.
In another more preferred aspect, the amino acid is lysine. In another more
preferred aspect,
the amino acid is serine. In another more preferred aspect, the amino acid is
threonine. See,
for example, Richard, A., and Margaritis, A., 2004, Empirical modeling of
batch fermentation
kinetics for poly(glutamic acid) production and other microbial biopolymers,
Biotechnology
and Bioengineering 87 (4): 501-515.
In another preferred aspect, the fermentation product is a gas. In another
more
preferred aspect, the gas is methane. In another more preferred aspect, the
gas is H2. In
another more preferred aspect, the gas is C02. In another more preferred
aspect, the gas is
-61-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
CO. See, for example, Kataoka, N., A. Miya, and K. Kiriyama, 1997, Studies on
hydrogen
production by continuous culture system of hydrogen-producing anaerobic
bacteria, Water
Science and Technology 36 (6-7): 41-47; and Gunaseelan V.N. in Biomass and
Bioenergy,
Vol. 13 (1-2), pp. 83-114, 1997, Anaerobic digestion of biomass for methane
production: A
review.
Recovery. The fermentation product(s) can be optionally recovered from the
fermentation medium using any method known in the art including, but not
limited to,
chromatography, electrophoretic procedures, differential solubility,
distillation, or extraction.
For example, alcohol is separated from the fermented cellulosic material and
purified by
conventional methods of distillation. Ethanol with a purity of up to about 96
vol.% can be
obtained, which can be used as, for example, fuel ethanol, drinking ethanol,
i.e., potable
neutral spirits, or industrial ethanol.
Signal Peptide
The present invention also relates to an isolated polynucleotide encoding a
signal
peptide comprising or consisting of amino acids 1 to 18 of SEQ ID NO: 2. The
polynucleotide
may further comprise a gene encoding a protein, which is operably linked to
the signal
peptide and/or propeptide. The protein is preferably foreign to the signal
peptide. In one
aspect, the polynucleotide for the signal peptide is nucleotides 1 to 54 of
SEQ ID NO: 1.
The present invention also relates to nucleic acid constructs, expression
vectors and
recombinant host cells comprising such polynucleotides.
The present invention also relates to methods of producing a protein,
comprising: (a)
cultivating a recombinant host cell comprising such polynucleotide; and (b)
recovering the
protein.
The protein may be native or heterologous to a host cell. The term "protein"
is not
meant herein to refer to a specific length of the encoded product and,
therefore,
encompasses peptides, oligopeptides, and polypeptides. The term "protein" also
encompasses two or more polypeptides combined to form the encoded product. The
proteins also include hybrid polypeptides and fused polypeptides.
Preferably, the protein is a hormone or variant thereof, enzyme, receptor or
portion
thereof, antibody or portion thereof, or reporter. For example, the protein
may be an
oxidoreductase, transferase, hydrolase, lyase, isomerase, or ligase such as an
aminopeptidase, amylase, carbohydrase, carboxypeptidase, catalase, cellulase,
chitinase,
cutinase, cyclodextrin glycosyltransferase, deoxyribonuclease, esterase, alpha-
galactosidase, beta-galactosidase, glucoamylase, alpha-glucosidase, beta-
glucosidase,
invertase, laccase, another lipase, mannosidase, mutanase, oxidase,
pectinolytic enzyme,
peroxidase, phytase, polyphenoloxidase, proteolytic enzyme, ribonuclease,
-62-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
transglutaminase or xylanase.
The gene may be obtained from any prokaryotic, eukaryotic, or other source.
The present invention is further described by the following examples that
should not
be construed as limiting the scope of the invention.
Examples
Chemicals used as buffers and substrates were commercial products of at least
reagent grade.
Strains
Aspergillus aculeatus strain NN000525 (IAM 2445, IAM Culture Collection,
Institute
of Molecular and Cellular Biosciences, The University of Tokyo) was used as a
source of a
GH6 polypeptide having cellobiohydrolase activity. Aspergillus oryzae JaL355
strain (WO
2005/070962) was used for expression of the Aspergillus aculeatus GH6
polypeptide having
cellobiohydrolase activity.
Media
Shake flask medium was composed of 15 g of glucose, 4 g of K2HPO4, 1 g of
NaCl,
0.2 g of MgSO4.7H2O, 2 g of MES free acid, 1 g of Bacto Peptone, 5 g of yeast
extract, 2.5 g
of citric acid, 0.2 g of CaCI2.2H2O, 5 g of NH4NO3, 1 ml of trace elements
solution, and
deionized water to 1 liter.
Trace elements solution was composed of 1.2 g of FeSO4.7H2O, 10 g of
ZnSO4.7H2O, 0.7 g of MnSO4=H2O, 0.4 g of CuSO4.5H2O, 0.4 g of Na2B4O7 10H2O,
0.8 g of
Na2MoO2.2H2O, and deionized water to 1 liter.
PDA plates were composed of 39 grams of potato dextrose agar and deionized
water
to 1 liter.
NNCYP-PCS medium was composed of 1 g of NaCl, 5 g of NH4NO3, 2 g of MES
hydrate, 2.75 g of citric acid, 0.2 g of CaCI2=H2O, 5 g of bacto peptone, 5 g
of yeast extract,
0.2 g of MgSO4.7H2O, 4 g of K2HPO4, 1 ml COVE trace metals solution, 2 g of
dextrose, 5%
w/v PCS (dilute acid pretreated corn stover pH 5), and deionized water to 1
liter.
COVE trace metals solution was composed 0.04 g of Na2B4O710H2O, 0.4 g of
CuSO4.5H2O, 1.2 g of FeSO4.7H2O, 0.7 g of MnSO4=H2O, 0.8 g of Na2MoO4.2H2O, 10
g of
ZnSO4.7H2O), and deionized water to 1 liter.
LB plates were composed of 10 g of tryptone, 5 g of yeast extract, 10 g of
sodium
chloride, 15 g of agar, and deionized water to 1 liter.
-63-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
YP medium was composed of 10 g of yeast extract, 20 g of Bacto peptone, and
deionized water to 1 liter.
YPM medium was composed of 10 g of yeast extract, 20 g of Bacto peptone, 20 g
of
maltose, and deionized water to 1 liter.
Example 1: Growth of wild-type Aspergillus aculeatus
Aspergillus aculeatus strain NN000525 was inoculated into 100 ml of shake
flask
medium in a 500 ml shake flask using two plugs from a PDA plate and incubated
at 45 C on
an orbital shaker at 200 rpm for 48 hours. Fifty ml of the shake flask medium
was used to
inoculate a 2 liter fermentation vessel.
Fermentation batch medium was composed of 5 g of yeast extract, 176 g of
powdered cellulose, 2 g of glucose, 1 g of NaCl, 1 g of Bacto Peptone, 4 g of
K2HPO4, 0.2 g
of CaC12.2H2O, 0.2 g of MgSO4.7H2O, 2.5 g of citric acid, 5 g of NH4NO3, 1.8
ml of anti-foam,
1 ml of trace elements solution, and deionized water to 1 liter. Fermentation
feed was
composed of water and antifoam.
A total of 1.8 liters of the fermentation batch medium was added to a two
liter glass
jacketed fermentor (Applikon Biotechnology, Schiedam, Netherlands).
Fermentation feed
medium was dosed at a rate of 4 g/l/hr for a period of 72 hours. The
fermentation vessel was
maintained at a temperature of 45 C and pH was controlled using an Applikon
1030 control
system (Applikon Biotechnology, Schiedam, Netherlands) to a set-point of 5.6
+/- 0.1. Air
was added to the vessel at a rate of 1 vvm and the broth was agitated by
Rushton impeller
rotating at 1100 to 1300 rpm. At the end of the fermentation, whole broth was
harvested from
the vessel and centrifuged at 3000 x g to remove the biomass.
Example 2: Purification of native CeI6A cellobiohydrolase from wild-type
Aspergillus
aculeatus whole broth
The harvested A. aculeatus broth obtained in Example 1 was centrifuged in 500
ml
bottles at 13,000 x g for 20 minutes at 4 C and then sterile filtered using a
0.22 pm
polyethersulfone membrane (Millipore, Bedford, MA, USA). The filtered broth
was
concentrated and buffer exchanged with 20 mM Tris-HCI pH 8.5 using a
tangential flow
concentrator (Pall Filtron, Northborough, MA, USA) equipped with a 10 kDa
polyethersulfone
membrane at approximately 20 psi. To decrease the amount of pigment, the
concentrate
was applied to a 60 ml Q SEPHAROSETM Big Bead column (GE Healthcare,
Piscataway,
NJ, USA) equilibrated with 20 mM Tris-HCI pH 8.5, and step eluted with
equilibration buffer
containing 0 to 600 mM NaCl. Flow-through and eluate fractions were examined
on 8-16%
CRITERION TM SDS-PAGE gels (Bio-Rad Laboratories, Inc., Hercules, CA, USA)
stained
with GELCODE Blue Stain Reagent (Thermo Fisher Scientific, Waltham, MA, USA).
The
-64-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
eluate fraction contained A. aculeatus Cel6A cellobiohydrolase as judged by
the presence of
a 70 kDa band corresponding to the apparent molecular weight of the Cel6A
cellobiohydrolase.
The eluate fraction was concentrated using an Amicon ultrafiltration device
(Millipore,
Bedford, MA, USA; 10 kDa polyethersulfone membrane, 40 psi, 4 C) and desalted
(HIPREPTM 26/10 desalting columns, GE Healthcare, Piscataway, NJ, USA) into 20
mM
Tris-HCI pH 8.5. The desalted material was loaded onto a MONO QTM column (HR
16/10,
GE Healthcare, Piscataway, NJ, USA) equilibrated with 20 mM Tris-HCI pH 8.5.
Bound
proteins were eluted with a salt gradient (20 column volumes) from 0 M NaCl to
600 mM
NaCl in 20 mM Tris-HCI pH 8.5. Fractions were examined by 8-16% SDS-PAGE gels
as
described above and revealed that the Aspergillus aculeatus Cel6A
cellobiohydrolase eluted
at approximately 50 mM NaCl.
Fractions containing Cel6A cellobiohydrolase were pooled and mixed with an
equal
volume of 20 mM Tris-HCI pH 7.5 containing 3.4 M ammonium sulfate for a final
concentration of 1.7 M ammonium sulfate. The sample was filtered (0.2 pM
syringe filter,
polyethersulfone membrane, Whatman, Maidstone, United Kingdom) to remove
particulate
matter prior to loading onto a 20 ml SOURCETM 15PHE column (GE Healthcare,
Piscataway,
NJ, USA) equilibrated with 1.7 M ammonium sulfate in 20 mM Tris-HCI pH 7.5.
Bound
proteins were eluted with a decreasing salt gradient (15 column volumes) from
1.7 M
ammonium sulfate to 0 M ammonium sulfate in 20 mM Tris-HCI pH 7.5. Fractions
were
analyzed by 8-16% SDS-PAGE gel electrophoresis as described above, which
revealed the
Cel6A cellobiohydrolase eluted at the very end of the gradient (approximately
50 mM
ammonium sulfate).
The A. aculeatus Cel6A cellobiohydrolase was greater than 90% pure as judged
by
SDS-PAGE. Protein concentrations were determined using a BCA Protein Assay Kit
(Thermo Fisher Scientific, Waltham, MA, USA) in which bovine serum albumin was
used as
a protein standard.
Example 3: Effect of Aspergillus aculeatus Family 6 cellobiohydrolase on PCS
hydrolysis
Corn stover was pretreated at the U.S. Department of Energy National Renewable
Energy Laboratory (NREL) using 1.4 wt % sulfuric acid at 165 C and 107 psi for
8 minutes.
The water-insoluble solids in the pretreated corn stover contained 57.5%
cellulose, 4.6%
hemicellulose and 28.4% lignin. Cellulose and hemicellulose were determined by
a two-
stage sulfuric acid hydrolysis with subsequent analysis of sugars by high
performance liquid
chromatography using NREL Standard Analytical Procedure #002. Lignin was
determined
gravimetrically after hydrolyzing the cellulose and hemicellulose fractions
with sulfuric acid
-65-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
using NREL Standard Analytical Procedure #003.
The pretreated corn stover was milled and washed with water prior to use.
Milled,
washed pretreated corn stover (initial dry weight 32.35%) was prepared by
milling in a
Cosmos ICMG 40 wet multi-utility grinder (EssEmm Corporation, Tamil Nadu,
India), and
subsequently washing repeatedly with deionized water and decanting off the
supernatant
fraction. The dry weight of the milled, water-washed pretreated corn stover
was found to be
7.114%.
A. aculeatus cellobiohydrolase was evaluated for its ability to enhance the
hydrolysis
of PCS by a Trichoderma reesei cellulolytic protein composition (Trichoderma
reesei broth
expressing Thermoascus aurantiacus GH61A and Aspergillus oryzae beta-
glucosidase
fusion; PCT/US2008/065417).
The hydrolysis of PCS was conducted using 2.2 ml deep-well plates (Axygen,
Union
City, CA, USA) in a total reaction volume of 1.0 ml. The hydrolysis was
performed with 50
mg of PCS per ml of 50 mM sodium acetate pH 5.0 buffer containing 1 mM
manganese
sulfate and a fixed protein loading of 2 mg of the T. reesei cellulolytic
protein preparation per
gram of cellulose or a 20% replacement (by protein) of the T. reesei
cellulolytic protein
preparation with A. aculeatus cellobiohydrolase enzyme (1.6 mg of the T.
reesei cellulolytic
protein composition per g of cellulose and 0.4 mg of each enzyme per g of
cellulose).
Hydrolysis assays were performed in triplicate for 72 hours at 50 C. Following
hydrolysis,
samples were filtered with a 0.45 pm Multiscreen 96-well filter plate
(Millipore, Bedford, MA,
USA) and filtrates analyzed for sugar content as described below.
When not used immediately, filtered sugary aliquots were frozen at -20 C.
Sugar
concentrations of samples diluted in 0.005 M H2SO4 were measured after elution
by 0.005 M
H2SO4 with 0.05% w/w benzoic acid at a flow rate of 0.6 ml per minute from a
4.6 x 250 mm
AMINEX HPX-87H column (Bio-Rad Laboratories, Inc., Hercules, CA, USA) at 65 C
with
quantitation by integration of the glucose and cellobiose signal from
refractive index
detection (CHEMSTATION , AGILENT 1100 HPLC, Agilent Technologies, Santa
Clara,
CA, USA) calibrated by pure sugar samples. The resultant equivalents were used
to
calculate the percentage of cellulose conversion for each reaction.
The degree of cellulose conversion was calculated using the following
equation:
% conversion = [glucose concentration + 1.053 x (cellobiose concentration)] /
[(glucose
concentration + 1.053 x (cellobiose concentration) in a limit digest]. The
1.053 factor for
cellobiose takes into account the increase in mass when cellobiose is
converted to glucose.
Fifty mg of the T. reesei cellulolytic protein preparation per g of cellulose
was used for the
limit digest.
The results shown in Figure 2 demonstrated that a 20% replacement (by protein)
of
the T. reesei cellulolytic protein preparation (loaded at 2 mg per g of
cellulose) with A.
-66-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
aculeatus cellobiohydrolase improved the 72 hour hydrolysis yield by 3.4%.
Alternatively, the
percent conversion with a 20% replacement of a T. reesei cellulolytic protein
preparation
(loaded at 2 mg per g of cellulose) with the A. aculeatus Cel6A
cellobiohydrolase was
equivalent to a loading of 2.15 mg of the T. reesei cellulolytic protein
preparation per g of
cellulose (a 1.08-fold improvement).
Example 4: Identification of an Aspergillus aculeatus Family 6
cellobiohydrolase
In-gel digestion of polypeptides for peptide sequencing. A MULTIPROBE II
Liquid Handling Robot (PerkinElmer Life and Analytical Sciences, Boston, MA,
USA) was
used to perform the in-gel digestions. The 70 kDa protein gel band described
in Example 2
was excised with a razor blade and reduced with 50 pl of 10 mM dithiothreitol
(DTT) in 100
mM ammonium bicarbonate pH 8.0 for 30 minutes. Following reduction, the gel
piece was
alkylated with 50 pl of 55 mM iodoacetamide in 100 mM ammonium bicarbonate pH
8.0 for
minutes. The dried gel piece was allowed to swell in 25 pl of a trypsin
digestion solution
15 containing 6 ng of sequencing grade trypsin (Promega, Madison, WI, USA) per
pl of 50 mM
ammonium bicarbonate pH 8 for 30 minutes at room temperature, followed by an 8
hour
digestion at 40 C. Each of the reaction steps described above was followed by
numerous
washes and pre-washes with the appropriate solutions following the
manufacturer's standard
protocol. Fifty pl of acetonitrile was used to de-hydrate the gel piece
between reactions and
20 the gel piece was air dried between steps. Peptides were extracted twice
with 1% formic
acid/2% acetonitrile in HPLC grade water for 30 minutes. Peptide extraction
solutions were
transferred to a 96 well skirted PCR type plate (ABGene, Rochester, NY, USA)
that had
been cooled to 10-15 C and covered with a 96-well plate lid (PerkinElmer Life
and Analytical
Sciences, Boston, MA, USA) to prevent evaporation. Plates were further stored
at 4 C until
mass spectrometry analysis was performed.
Protein Identification. For de novo peptide sequencing by tandem mass
spectrometry, a Q-TOFMICROTM (Waters Micromass MS Technologies, Milford, MA,
USA),
a hybrid orthogonal quadrupole time-of-flight mass spectrometer, was used for
LC/MS/MS
analysis. The Q-TOF MICROTM is fully microprocessor controlled using
MASSLYNXTM
software version 4.1 (Waters Micromass MS Technologies, Milford, MA, USA). The
Q-TOF
MICROTM was fitted with a NANOACQUITY UPLC (Waters Corp, Milford, MA, USA)
for
concentrating and desalting samples. Samples were loaded onto a trapping
column (180 .tm
ID X 20 mm, 5 m SYMMETRY C18) (Waters Corp, Milford, MA, USA) fitted in the
injection
loop and washed with 0.1% formic acid in water at 15 pl per minute for 1
minute using the
binary solvent manager pump. Peptides were separated on a 100 pm ID x 100 mm,
C18, 1.7
m, BEH130TM C18 nanoflow fused capillary column (Waters Corp, Milford, MA,
USA) at a
-67-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
flow rate of 400 nI per minute. A step elution gradient of 1% to 85%
acetonitrile in 0.1%
formic acid was applied over a 30 minute interval. The column eluent was
monitored at 214
nm and introduced into the Q-TOF MICROTM through an electrospray ion source
fitted with
the nanospray interface.
Data was acquired in survey scan mode from a mass range of m/z 400 to 1990
with
switching criteria for MS to MS/MS to include an ion intensity of greater than
10.0 counts per
second and charge states of +2, +3, and +4. Analysis spectra of up to 6 co-
eluting species
with a scan time of 1.9 seconds and inter-scan time of 0.1 seconds could be
obtained. A
cone voltage of 45 volts was typically used and the collision energy was
programmed to be
varied according to the mass and charge state of the eluting peptide and in
the range of
10-60 volts. The acquired spectra were combined, smoothed, and centered in an
automated
fashion and a peak list generated. The peak list was searched against selected
databases
using PROTEINLYNX GLOBAL SERVERTM 2.3 software (Waters Micromass MS
Technologies, Milford, MA, USA) and PEAKS Studio version 4.5 (SP1)
(Bioinformatic
Solutions Inc., Waterloo, Ontario, Canada). Results from the PROTEINLYNX
GLOBAL
SERVERTM and PEAKS Studio searches were evaluated and un-identified proteins
were
analyzed further by evaluating the MS/MS spectrums of each ion of interest and
de novo
sequence was determined by identifying the y and b ion series and matching
mass
differences to the appropriate amino acid.
Peptide sequences were obtained from several multiple charged ions for the in-
gel
digested 70 kDa polypeptide gel band. A doubly charged tryptic peptide ion of
404.233 m/z
sequence was determined to be Phe-[Ile/Leu]-Val-Asp-Thr-Gly-Arg (amino acids
370 to 376
of SEQ ID NO: 2). Another doubly charged tryptic peptide ion of 419.2206 m/z
sequence
was determined to be Ala-Tyr-[Ile/Leu]-Asp-Ser-[Ile/Leu]-Arg (amino acids 221
to 227 of
SEQ ID NO: 2). Another doubly charged tryptic peptide ion of 486.313 m/z
sequence was
determined to be [Ile/Leu]-Val-Thr-Asn-[Ile/Leu]-Asn-Val-Ala-Lys (amino acids
250 to 258 of
SEQ ID NO: 2). Another doubly charged tryptic peptide ion of 514.793 m/z
sequence was
determined to be Ala-Asn-[l le/Leu]-Tyr-Ala-Ser-Val-Tyr-Lys (amino acids 304
to 312 of SEQ
ID NO: 2). Another doubly charged tryptic peptide ion of 575.817 m/z sequence
was
determined to be Ser-[I le/Leu]-Ala-Asn-Asn-Gly-Val-Ala-Asn-Tyr-Lys (amino
acids 210 to
220 of SEQ ID NO: 2). Another double charged tryptic peptide of 666.3743 was
determined
to be Val-Pro-Ser-Phe-Val-Trp-Leu-Asp-Val-Ala-Ala-Lys (amino acids 152 to 163
of SEQ ID
NO:2). Another doubly charged tryptic peptide ion of 669.881 m/z a was
determined to be
Val-Pro-Thr-Met-Ala-Thr-Tyr-[Ile/Leu]-Ala-Asp-[Ile/Leu]-Lys (amino acids 164
to 175 of SEQ
ID NO: 2). [Ile/Leu] could not be distinguished because they have equivalent
masses.
-68-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
Example 5: Preparation of Aspergillus aculeatus strain NN000525 mycelia for
cDNA
library production
A. aculeatus strain NN000525 was inoculated onto a PDA plate and incubated for
4
days at 37 C in the darkness. Several mycelia-PDA plugs were inoculated into
500 ml shake
flasks containing 150 ml of NNCYP-PCS medium. The flasks were incubated for 4
days at
26 C with shaking at 120 rpm. The mycelia from the solid media were collected
and frozen in
liquid nitrogen and then stored in a -80 C freezer until use.
Example 6: Aspergillus aculeatus strain NN000525 RNA isolation
The frozen mycelia were transferred into a liquid nitrogen prechilled mortar
and
pestle and ground to a fine powder with a small amount of baked quartz sand.
Total RNA
was prepared from the powdered mycelia by extraction with TRIZOL LS
(Invitrogen Corp.,
Carlsbad, CA, USA) followed by triple extraction with chloroform and
precipitation with 0.7
v/v isopropanol. The total RNA pellet was redissolved in RNAase free water and
stored in a
-80 C freezer until use.
Example 7: Construction of Aspergillus aculeatus strain NN000525 cDNA
Double stranded cDNA was synthesized using a SMART TM PCR cDNA Synthesis Kit
(Clontech, Saint-Germain-en-Laye, France) according to the manufacturer's LD
PCR cDNA
amplification protocol.
Example 8: Isolation of the cDNA encoding Aspergillus aculeatus strain
NN000525
GH6 polypeptide
PCR was used to amplify a fragment of the cDNA containing the 5' end using the
SMART TM II A oligonucleotide (Clontech, Saint-Germain-en-Laye, France) and
the following
degenerate primers (TAG Copenhagen, Denmark):
Primer #578:
5'-GAGCAGTCTCGGTCGGGNADRTTRTA-3' (SEQ ID NO: 135)
Primer #580:
5'-GCCGTCGGACTCGCCNCCNGGYTT-3' (SEQ ID NO: 136)
The amplification reaction was composed of 1 pl of Aspergillus aculeatus
strain
NN000525 SMART TM cDNA, 12.5 pl of 2X REDDYMIXTM PCR Buffer (Thermo Fisher
Scientific Inc., Waltham, MA, USA), 1 pl of SMART TM II A oligonucleotide, 9.5
pl of H2O, and
1 pl of a 5 pM solution of either primer #578 or primer #580. The
amplification reactions were
incubated in a PTC-200 DNA ENGINETM Thermal Cycler (MJ Research Inc., Waltham,
MA,
USA) programmed for 1 cycle at 94 C for 2 minutes; and 35 cycles each at 94 C
for 15
seconds and 60 C for 1 minute.
-69-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
A 0.9 kb PCR reaction product and a 1.3 kb PCR reaction product were isolated
by
1% agarose gel electrophoresis using TAE buffer (40 mM Tris base-20 mM sodium
acetate-
1 mM disodium EDTA) and staining with SYBR Safe DNA gel stain (Invitrogen
Corp.,
Carlsbad, CA, USA). The DNA bands were visualized with the aid of an EAGLE EYE
Imaging System (Stratagene, La Jolla, CA, USA) and a DARKREADER
Transilluminator
(Clare Chemical Research, Dolores, CO, USA). The 0.9 and 1.3 kb DNA bands were
excised from the gels and purified using a GFX PCR DNA and Gel Band
Purification Kit
(GE Healthcare Life Sciences, Piscataway, NJ, USA) according to the
manufacturer's
instructions. The 0.9 kb band was sequenced with the #578 primer and the 1.3
kb fragment
was sequenced using the #580 primer.
The 3' end of the cDNA was amplified using the CDSIII oligonucleotide
(Clontech,
Saint-Germain-en-Laye, France) together with either of the following primers
(TAG
Copenhagen, Denmark):
Primer #601:
5'-CTCCTACACCCAGGGCAACA-3' (SEQ ID NO: 137)
Primer #602:
5'-CGATTGGTGCAACGTCATCA-3' (SEQ ID NO: 138)
The amplification reactions were composed of 1 pl of A. aculeatus strain
NN000525
SMART cDNA, 12.5 pl of 2X REDDYMIXTM PCR Buffer, 9.5 pl of H2O, and 1 pl of a
5 pM
solution of primer #601 or primer #602. The amplification reactions were
incubated in a PTC-
200 DNA ENGINETM Thermal Cycler programmed for 1 cycle at 94 C for 2 minutes;
and 35
cycles each at 94 C for 15 seconds and 60 C for 1 minute.
A 0.6 kb PCR reaction product and a 0.4 kbp PCR reaction product were isolated
by
1% agarose gel electrophoresis using TAE buffer and staining with SYBR Safe
DNA gel
stain. The DNA bands were visualized with the aid of an EAGLE EYE Imaging
System and
a DARKREADER Transilluminator. The 0.6 kb and a 0.4 kb DNA bands were excised
from
the gelsl and purified using a GFX PCR DNA and Gel Band Purification Kit
according to the
manufacturer's instructions. Both fragments were sequenced using primer #602.
Example 9: Characterization of the Aspergillus aculeatus strain NN000525 cDNA
sequence encoding a Family GH6 polypeptide having cellobiohydrolase activity
The nucleotide sequence (SEQ ID NO: 1) and deduced amino acid sequence (SEQ
ID NO: 2) of the cDNA encoding the A. aculeatus GH6 polypeptide having
cellobiohydrolase
activity are shown in Figures 1A and 1B. The open reading frame is 1407 bp
including the
stop codon, and encodes a polypeptide of 469 amino acids. The % G+C content of
the full-
length coding sequence and the mature coding sequence is 61.9% and 62.0%,
respectively.
Using the SignalP software program (Nielsen et al., 1997, Protein Engineering
10: 1-6), a
-70-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
signal peptide of 18 residues was predicted. The predicted mature protein
contains 451
amino acids with a molecular mass of 47 kDa.
Analysis of the deduced amino acid sequence of the GH6 polypeptide having
cellobiohydrolase activity with the Interproscan program (Mulder et al., 2007,
Nucleic Acids
Res. 35: D224-D228) showed that the GH6 polypeptide contained the sequence
signature of
glycoside hydrolase family 6 (InterPro accession IPR001524). This sequence
signature was
found from approximately residues 90 to 451 of the mature polypeptide (Pfam
accession
PF01341). The Interproscan program analysis also revealed a CBM 1 cellulose
binding
domain (InterPro accession IPR000254). This sequence signature was found from
approximately residues 4 to 37 of the mature polypeptide (Pfam accession
PF01341).
A comparative pairwise global alignment of amino acid sequences was determined
using the Needleman-Wunsch algorithm (Needleman and Wunsch, 1970, J. Mol.
Biol. 48:
443-453) as implemented in the Needle program of EMBOSS with gap open penalty
of 10,
gap extension penalty of 0.5, and the EBLOSUM62 matrix. The alignment showed
that the
deduced amino acid sequence of the A. aculeatus GH6 mature polypeptide shared
98%
identity (excluding gaps) to the deduced amino acid sequence of a fungal
Family 6 glycoside
hydrolase protein (GeneSeqP accession number ASR94299).
Example 10: Cloning of the Aspergillus aculeatus strain NN000525 GH6
polypeptide
encoding cDNA
Based on the cDNA sequence, oligonucleotide primers, shown below, were
designed
to amplify the GH6 gene from cDNA of A. aculeatus strain NN000525.
Primer #609:
5'-TAAGAATTCACCATGCGTTATACATTGTCTCTCGCA3' (SEQ ID NO: 139)
Primer #608:
5'-TATGCGGCCGCYTARAANGCNGGRTTNGCRTT-3' (SEQ ID NO: 140)
The amplification reaction was composed of 1 pl of Aspergillus aculeatus
strain
NN000525 SMART cDNA, 12.5 pl of 2X REDDYMIXTM PCR Buffer, 1 pl of 5 pM primer
#609, 1 pl of 5 pM primer #608, and 9.5 pl of H2O. The amplification reaction
was incubated
in a PTC-200 DNA ENGINETM Thermal Cycler programmed for 1 cycle at 94 C for 2
minutes; and 35 cycles each at 94 C for 15 seconds and 60 C for 1.5 minutes.
A 1.4 kb PCR reaction product was isolated by 1 % agarose gel electrophoresis
using
TAE buffer and staining with SYBR Safe DNA gel stain. The DNA band was
visualized with
the aid of an EAGLE EYE Imaging System and a DARKREADER Transilluminator.
The
1.4 kb DNA band was excised from the gel and purified using a GFX PCR DNA and
Gel
Band Purification Kit according to the manufacturer's instructions.
The 1.4 kb fragment was cleaved with Eco RI and Not I and purified using a GFX
-71-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
PCR DNA and Gel Band Purification Kit according to the manufacturer's
instructions.
The cleaved 1.4 kb fragment was then directionally cloned by ligation into Eco
RI-Not
I cleaved pXYG1051 (WO 2005/080559) using T4 ligase (Promega, Madison, WI,
USA)
according to the manufacturer's instructions. The ligation mixture was
transformed into E.
coli TOP10F competent cells (Invitrogen Corp., Carlsbad, CA, USA) according to
the
manufacturer's instructions. The transformation mixture was plated onto LB
plates
supplemented with 100 pg of ampicillin per ml. Plasmid minipreps were prepared
from
several transformants and sequenced. One plasmid with the correct Aspergillus
aculeatus
GH6 coding sequence was chosen. The plasmid was designated pXYG1051-P6XY
(Figure
3). The expression vector pXYG1051 contains the same neutral amylase II (NA2)
promoter
derived from Aspergillus niger, and terminator elements as pCaHj483 (disclosed
in Example
4 of WO 98/00529). Furthermore pXYG1051 has pUC18 derived sequences for
selection
and propagation in E. coli, and pDSY82 (disclosed in Example 4 of U.S. Patent
No.
5,958,727) derived sequences for selection and expression in Aspergillus
facilitated by the
pyrG gene of Aspergillus oryzae, which encodes orotidine decarboxylase and is
used to
complement a pyrG mutant Aspergillus strain.
The 1.4 kb fragment PCR amplified by primers #609 and #608 was also cloned by
ligation into pCR 2.1 (Invitrogen, Carlsbad, CA, USA) digested with Eco RI and
Not I using
standard molecular biology techniques to yield pCR2.1-P6XY (Figure 4). The
Aspergillus
aculeatus GH6 polypeptide gene insert in pCR2.1-P6XY was determined by Sanger
sequencing to encode the same polypeptide sequence as in pXYG1051-P6XY, but
varied at
several positions (SEQ ID NO: 141) corresponding to the wobble bases of primer
#608.
These changes can easily be corrected by site-directed mutagenesis. E. coli
NN059164
containing pCR2.1-P6XY was deposited with the Deutsche Sammlung von
Mikroorganismen
and Zellkulturen GmbH (DSM) on October 1, 2009 and assigned accession number
DSM
22994.
Example 11: Production of recombinant Aspergillus aculeatus GH6 polypeptide
having cellobiohydrolase activity in Aspergillus oryzae
The expression plasmid pXYG1051-P6XY was transformed into Aspergillus oryzae
JaL355 as described in WO 98/00529. Transformants were purified on selection
plates
through single conidia prior to sporulating them on PDA plates. Production of
the Aspergillus
aculeatus GH6 polypeptide by the transformants was analyzed from culture
supernatants of
1 ml 96 deep well stationary cultivations at 26 C in YP medium with 2%
maltodextrin.
Expression was verified on NUPAGE 10% Bis-Tris SDS-PAGE (Invitrogen,
Carlsbad, CA,
USA) by Coomassie blue staining. One transformant was selected for further
work and
designated Aspergillus oryzae 86.10.
-72-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
For larger scale production, Aspergillus oryzae 86.10 spores were spread onto
a
PDA plate and incubated for five days at 37 C. The confluent spore plate was
washed twice
with 5 ml of 0.01% TWEEN 20 to maximize the number of spores collected. The
spore
suspension was then used to inoculate twenty-five 500 ml flasks containing 100
ml of YPM
medium. The culture was incubated at 30 C with constant shaking at 85 rpm. At
day four
post-inoculation, the culture broth was collected by filtration through a
triple layer of
Whatman glass microfiber filters of 1.6 pm, 1.2 pm, and 0.7 pm. Fresh culture
broth from this
transformant produced a band of GH6 protein of approximately 70 kDa.
Example 12: Purification of recombinant Aspergillus aculeatus CeI6A
cellobiohydrolase
One liter of harvested broth (Example 11) was sterile filtered using a 0.22 pm
polyethersulfone membrane (Millipore, Bedford, MA, USA). Ammonium sulfate was
added to
the filtered broth to 2 M ammonium sulfate as a final concentration and
applied to a 70 ml
PHENYL SEPHAROSETM Fast Flow column (GE Healthcare, Piscataway, NJ, USA). The
column was washed with 3 column volumes of 2 M ammonium sulfate and then 5
column
volumes of 1 M ammonium sulfate. Bound proteins were eluted with a decreasing
salt
gradient (2 column volumes) of 1 M ammonium sulfate to 0 M ammonium sulfate in
20 mM
HEPES pH 7Ø Fractions were analyzed by SDS-PAGE using 4-20% NUPAGE
Bis/Tris,
SDS-PAGE gels (Invitrogen Corporation, Carlsbad, CA, USA) stained with
INSTANTBLUETM
Stain (Expedeon Protein Solutions, Cambridge, UK). The eluate fractions
containing A.
aculeatus CeI6A cellobiohydrolase as judged by the presence of a 65-70 kDa
band
corresponding to the apparent molecular weight of the CeI6A cellobiohydrolase
were pooled
and desalted (500 ml SEPHADEXTM G-25 Medium column, GE Healthcare, Piscataway,
NJ,
USA) into 20 mM HEPES pH 7.5.
The desalted material was applied to a 20 ml SOURCETM 15Q column (GE
Healthcare, Piscataway, NJ, USA) equilibrated with 20 mM HEPES pH 7.5. Bound
proteins
were eluted with a salt gradient (10 column volumes) from 0 M NaCl to 500 mM
NaCl in 50
mM HEPES pH 7.5. Flow through and eluate fractions were examined by SDS-PAGE
using
4-20% NUPAGE Bis/Tris, SDS-PAGE gels stained with INSTANTBLUETM Stain. The
flow-
through fraction contained A. aculeatus CeI6A cellobiohydrolase and was
concentrated
(VIVASPINTM 20, 10kDa membrane, Sartorius Stedim Biotech S.A., Aubagne,
France).
The A. aculeatus CeI6A cellobiohydrolase was greater than 90% pure as judged
by
SDS-PAGE. Protein concentrations were determined by the absorbance at 280 nm
using an
extinction coefficient of 1.54 (ml)(cm-')(mg-1).
Example 13: Effect of recombinant Aspergillus aculeatus CeI6A
cellobiohydrolase on
-73-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
PCS hydrolysis
Corn stover was pretreated at the U.S. Department of Energy National Renewable
Energy Laboratory (NREL) using 0.048 g sulfuric acid/ g dry biomass at 190 C
and 25% w/w
dry solids for approximately 1 minute. The water-insoluble solids in the
pretreated corn
stover contained 52% cellulose, 3.6% hemicellulose and 29.8% lignin. Cellulose
and
hemicellulose were determined by a two-stage sulfuric acid hydrolysis with
subsequent
analysis of sugars by high performance liquid chromatography using NREL
Standard
Analytical Procedure #002. Lignin was determined gravimetrically after
hydrolyzing the
cellulose and hemicellulose fractions with sulfuric acid using NREL Standard
Analytical
Procedure #003. The pretreated corn stover was ground using a Multi Utility
Grinder (iNNo
Concepts Inc., Roswell, GA, USA) and sieved through a Sieve Shaker AS200
equipped with
a 450 pm screen (Retsch, Inc. Newtown, PA, USA) and designated herein as GS-
PCS.
The recombinant A. aculeatus cellobiohydrolase purified according to Example
12
was evaluated for its ability to enhance the hydrolysis of GS-PCS by CELLICTM
CTec (a
cellulolytic protein composition available from Novozymes A/S, Bagsvaerd,
Denmark). The
protein concentration was determined by a BCA reagent Kit (Pierce, Rockford,
IL, USA).
Hydrolysis of GS-PCS was performed in 96 well plates in a total reaction
volume of
1.0 ml. The hydrolysis was performed with 50 mg of GS-PCS per ml of 50 mM
sodium
acetate pH 5.0 buffer containing 1 mM manganese sulfate and 3 mg of CELLICTM
CTec per
gram of cellulose and 0.6 mg of the A. aculeatus cellobiohydrolase per gram of
cellulose for
a total loading of 3.6 mg protein per g cellulose. The hydrolysis assays were
performed in
duplicate for 72 hours at 50 C. Following hydrolysis, samples were filtered
with a 0.45 pm
Multiscreen 96-well filter plate (Millipore, Bedford, MA, USA), diluted 2-fold
in 5 mM H2SO4,
and analyzed by HPLC as described below. Sugar concentrations were measured
after
elution by 0.005 M H2SO4 with 0.05% w/w benzoic acid at a flow rate of 0.6 ml
per minute
from a 4.6 x 250 mm AMINEX HPX-87H column at 65 C using refractive index
detection.
Hydrolysis data are presented as % of total cellulose converted to glucose.
The degree of
cellulose conversion to reducing sugar was calculated using the following
equation:
Conversion (%) = RS (,,g/,,,) * 100 * 162 / (Cellulose (,,g/,,,) * 180) _
RS (,,g/,,,) * 100 / (Cellulose (,,g/,,,) * 1.111)
In this equation, RS is the concentration of reducing sugar in solution
measured in glucose
equivalents (mg/ml), and the factor 1.111 reflects the weight gain in
converting cellulose to
glucose.
The results demonstrated that the A. aculeatus GH6 cellobiohydrolase at 0.6
mg/g
cellulose and CELLICTM CTec at 3 mg/g cellulose yieled a cellulose conversion
of 64.7%
after 72 hours, while CELLICTM CTec alone at 3 mg/g cellulose yielded a
cellulose
conversion of 58.6%, CELLICTM CTec alone at 3.6 mg/g cellulose yielded a
cellulose
-74-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
conversion of 66.8%, and the A. aculeatus GH6 cellobiohydrolase alone at 0.6
mg/g
cellulose yieled a cellulose conversion of 1%. The A. aculeatus GH6
cellobiohydrolase had
synergistic effect on CELLICTM CTec in GS-PCS hydrolysis at 50 C, pH 5Ø
Example 13: Characterization of Aspergillus aculeatus GH6 cellobiohydrolase
Specific activity: Phosphoric acid swollen cellulose (PASC) was dissolved in
50 mM
sodium acetate pH 5 with 0.01% TWEEN 20 at 2.1 g per liter. Enzyme was
diluted in the
same buffer to a range of dilutions. To 190 pl of the PASC solution was added
10 pl of each
enzyme dilution. The reaction was incubated at 50 C for 30 minutes before the
reaction was
stopped with 50 pl of 0.5 M sodium hydroxide followed by centrifugation at 800
x g for 5
minutes. Supernatant was removed and reducing sugar was measured using p-
hydroxybenzoic acid hydrazide (PHBAH) reagent according to Lever, 1973,
Biochem. Med.
7:274-287. An enzyme control, reagent control and substrate control were
included. The
absorbance at 405 nm was measured for 4-nitrophenolate production. The
specific activity of
the A. aculeatus GH6 cellobiohydrolase on PASC was determined to be 1.6 IU/mg.
Thermostability: The A. aculeatus GH6 cellobiohydrolase was diluted in 50 mM
sodium acetate pH 5 containing 0.01% TWEEN 20 to 1 mg per ml, and then
incubated at
50 C for 3 days and 60 C for 3 hours and 24 hours. The same sample was stored
at 4 C to
serve as control. After incubation, the activity of the samples on PASC was
measured as
described above using one enzyme loading which gave less than 5% conversion.
The
activity of the sample at 4 C was normalized to 100%, and the activities of
the other samples
at other incubation conditions were compared to the 4 C activity. The
thermostability of the
A. aculeatus GH6 cellobiohydrolase is shown below.
Incubation conditions Residual % Activity
4 C 100%
50 C, 72 hr 100%
60 C, 3 hr 52%
60 C, 24 hr 0%
pH profile: The pH activity profile of the A. aculeatus GH6 cellobiohydrolase
was
determined using the same protocol described above, except the
cellobiohydrolase was
incubated at five different pHs (4, 5, 6, 7, and 8) and one enzyme loading was
used, which
yielded less than 5% conversion. Britton Robinson buffer (100 mM) was used as
the buffer
system. The 100 mM Britton Robinson buffer was titrated to a various pH values
in the range
of 4-7 using 5 M sodium hydroxide and then diluted to 40 mM with deionized
water. PASC
was prepared in the same buffers. Cellobiohydrolase activity was measured at
50 C. The
highest activity was normalized to be 100%, and activities at other pH values
were compared
-75-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
to the highest activity and expressed in % activity. The pH profile of the A.
aculeatus GH6
cellobiohydrolase is shown below.
Relative %
pH Activity
4.0 43%
5.0 93%
6.0 100%
7.0 90%
8.0 70%
Deposit of Biological Material
The following biological material has been deposited under the terms of the
Budapest
Treaty with the Deutsche Sammlung von Mikroorganismen and Zellkulturen GmbH
(DSM),
Mascheroder Weg 1 B, D-38124 Braunschweig, Germany, and given the following
accession
number:
Deposit Accession Number Date of Deposit
E. coli DSM 22994 October 1, 2009
The strain has been deposited under conditions that assure that access to the
culture
will be available during the pendency of this patent application to one
determined by foreign
patent laws to be entitled thereto. The deposit represents a substantially
pure culture of the
deposited strain. The deposit is available as required by foreign patent laws
in countries
wherein counterparts of the subject application, or its progeny are filed.
However, it should
be understood that the availability of a deposit does not constitute a license
to practice the
subject invention in derogation of patent rights granted by governmental
action.
The present invention is further described by the following numbered
paragraphs:
[1] An isolated polypeptide having cellobiohydrolase activity, selected from
the group
consisting of: (a) a polypeptide comprising an amino acid sequence having at
least 99%
identity to the mature polypeptide of SEQ ID NO: 2; (b) a polypeptide encoded
by a
polynucleotide comprising a nucleotide sequence having at least 99% identity
to the mature
polypeptide coding sequence of SEQ ID NO: 1; and (c) a polypeptide comprising
the mature
polypeptide of SEQ ID NO: 2, or a fragment thereof having cellobiohydrolase
activity.
[2] The polypeptide of paragraph 1, comprising an amino acid sequence having
at
least 99% identity to the mature polypeptide of SEQ ID NO: 2.
[3] The polypeptide of paragraph 1, comprising or consisting of the amino acid
sequence of SEQ ID NO: 2; or a fragment thereof having cellobiohydrolase
activity.
-76-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
[4] The polypeptide of paragraph 1, comprising or consisting of the amino acid
sequence of SEQ ID NO: 2.
[5] The polypeptide of paragraph 1, comprising or consisting of the mature
polypeptide of SEQ ID NO: 2.
[6] The polypeptide of paragraph 1, which is encoded by a polynucleotide
comprising
a nucleotide sequence having at least 99% identity to the mature polypeptide
coding
sequence of SEQ ID NO: 1
[7] The polypeptide of paragraph 1, which is encoded by a polynucleotide
comprising
or consisting of the nucleotide sequence of SEQ ID NO: 1; or a subsequence
thereof
encoding a fragment having cellobiohydrolase activity.
[8] The polypeptide of paragraph 7, which is encoded by a polynucleotide
comprising
or consisting of the nucleotide sequence of SEQ ID NO: 1.
[9] The polypeptide of paragraph 7, which is encoded by a polynucleotide
comprising
or consisting of the mature polypeptide coding sequence of SEQ ID NO: 1.
[10] The polypeptide of paragraph 1, which is encoded by the polynucleotide
contained in plasmid pCR2.1-P6XY which is contained in E. coli DSM 22994.
[11] The polypeptide of any of paragraphs 1-12, wherein the mature polypeptide
is
amino acids 19 to 469 of SEQ ID NO: 2.
[12] The polypeptide of any of paragraphs 1-13, wherein the mature polypeptide
coding sequence is nucleotides 55 to 1407 of SEQ ID NO: 1.
[13] An isolated polynucleotide comprising a nucleotide sequence that encodes
the
polypeptide of any of paragraphs 1-12.
[14] A nucleic acid construct comprising the polynucleotide of paragraph 13
operably
linked to one or more (several) control sequences that direct the production
of the
polypeptide in an expression host.
[15] A recombinant expression vector comprising the polynucleotide of
paragraph 13.
[16] A recombinant host cell comprising the polynucleotide of paragraph 13
operably
linked to one or more (several) control sequences that direct the production
of a polypeptide
having cellobiohydrolase activity.
[17] A method of producing the polypeptide of any of paragraphs 1-12,
comprising:
(a) cultivating a cell, which in its wild-type form produces the polypeptide,
under conditions
conducive for production of the polypeptide; and (b) recovering the
polypeptide.
[18] A method of producing the polypeptide of any of paragraphs 1-12,
comprising:
(a) cultivating a host cell comprising a nucleic acid construct comprising a
polynucleotide
encoding the polypeptide under conditions conducive for production of the
polypeptide; and
(b) recovering the polypeptide.
[19] A method of producing a mutant of a parent cell, comprising disrupting or
-77-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
deleting a polynucleotide encoding the polypeptide, or a portion thereof, of
any of
paragraphs 1-12, which results in the mutant producing less of the polypeptide
than the
parent cell.
[20] A mutant cell produced by the method of paragraph 19.
[21] The mutant cell of paragraph 20, further comprising a gene encoding a
native or
heterologous protein.
[22] A method of producing a protein, comprising: (a) cultivating the mutant
cell of
paragraph 21 under conditions conducive for production of the protein; and (b)
recovering
the protein.
[23] A method of producing the polypeptide of any of paragraphs 1-12,
comprising:
(a) cultivating a transgenic plant or a plant cell comprising a polynucleotide
encoding the
polypeptide under conditions conducive for production of the polypeptide; and
(b) recovering
the polypeptide.
[24] A transgenic plant, plant part or plant cell transformed with a
polynucleotide
encoding the polypeptide of any of paragraphs 1-12.
[25] A double-stranded inhibitory RNA (dsRNA) molecule comprising a
subsequence
of the polynucleotide of paragraph 13, wherein optionally the dsRNA is a siRNA
or a miRNA
molecule.
[26] The double-stranded inhibitory RNA (dsRNA) molecule of paragraph 25,
which is
about 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or more duplex nucleotides in
length.
[27] A method of inhibiting the expression of a polypeptide having
cellobiohydrolase
activity in a cell, comprising administering to the cell or expressing in the
cell the double-
stranded inhibitory RNA (dsRNA) molecule of paragraph 25 or 26.
[28] An isolated polynucleotide encoding a signal peptide comprising or
consisting of
amino acids 1 to 18 of SEQ ID NO: 2.
[29] A nucleic acid construct comprising a gene encoding a protein operably
linked to
the polynucleotide of paragraph 28, wherein the gene is foreign to the
polynucleotide.
[30] A recombinant expression vector comprising the polynucleotide of
paragraph 28.
[31] A recombinant host cell comprising the polynucleotide of paragraph 28.
[32] A method of producing a protein, comprising: (a) cultivating a
recombinant host
cell comprising a gene encoding a protein operably linked to the
polynucleotide of paragraph
28, wherein the gene is foreign to the polynucleotide, under conditions
conducive for
production of the protein; and (b) recovering the protein.
[33] A composition comprising the polypeptide of any of paragraphs 1-12.
[34] The composition of paragraph 33, which further comprises one or more
(several)
enzymes selected from the group consisting of a cellulase, a GH61 polypeptide
having
cellulolytic enhancing activity, a hemicellulase, an expansin, an esterase, a
laccase, a
-78-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
ligninolytic enzyme, a pectinase, a peroxidase, a protease, and a swollenin.
[35] A method for degrading or converting a cellulosic material, comprising:
treating
the cellulosic material with an enzyme composition in the presence of the
polypeptide of any
of paragraphs 1-12.
[36] The method of paragraph 35, wherein the cellulosic material is
pretreated.
[37] The method of paragraph 35 or 36, further comprising recovering the
degraded
cellulosic material.
[38] The method of any of paragraphs 35-37, wherein the enzyme composition
comprises one or more (several) enzymes selected from the group consisting of
a cellulase,
a GH61 polypeptide having cellulolytic enhancing activity, a hemicellulase, an
expansin, an
esterase, a laccase, a ligninolytic enzyme, a pectinase, a peroxidase, a
protease, and a
swollenin.
[39] The method of paragraph 38, wherein the cellulase one or more (several)
enzymes selected from the group consisting of an endoglucanase, a
cellobiohydrolase, and
a beta-glucosidase.
[40] The method of paragraph 38, wherein the hemicellulase is one or more
(several)
enzymes selected from the group consisting of a xylanase, an acetyxylan
esterase, a feruloyl
esterase, an arabinofuranosidase, a xylosidase, and a glucuronidase.
[41] The method of any of paragraphs 35-40, wherein the degraded cellulosic
material is a sugar.
[42] The method of paragraph 41, wherein the sugar is selected from the group
consisting of glucose, xylose, mannose, galactose, and arabinose.
[43] A method for producing a fermentation product, comprising: (a)
saccharifying a
cellulosic material with an enzyme composition in the presence of the
polypeptide of any of
paragraphs 1-12; (b) fermenting the saccharified cellulosic material with one
or more
fermenting microorganisms to produce the fermentation product; and (c)
recovering the
fermentation product from the fermentation.
[44] The method of paragraph 43, wherein the cellulosic material is
pretreated.
[45] The method of paragraph 43 or 44, wherein the enzyme composition
comprises
one or more (several) enzymes selected from the group consisting of a
cellulase, a GH61
polypeptide having cellulolytic enhancing activity, a hemicellulase, an
expansin, an esterase,
a laccase, a ligninolytic enzyme, a pectinase, a peroxidase, a protease, and a
swollenin.
[46] The method of paragraph 45, wherein the cellulase is one or more
(several)
enzymes selected from the group consisting of an endoglucanase, a
cellobiohydrolase, and
a beta-glucosidase.
[47] The method of paragraph 45, wherein the hemicellulase is one or more
(several)
enzymes selected from the group consisting of a xylanase, an acetyxylan
esterase, a feruloyl
-79-
CA 02776336 2012-03-30
WO 2011/059740 PCT/US2010/054484
esterase, an arabinofuranosidase, a xylosidase, and a glucuronidase.
[48] The method of any of paragraphs 43-47, wherein steps (a) and (b) are
performed simultaneously in a simultaneous saccharification and fermentation.
[49] The method of any of paragraphs 43-48, wherein the fermentation product
is an
alcohol, an organic acid, a ketone, an amino acid, or a gas.
[50] A method of fermenting a cellulosic material, comprising: fermenting the
cellulosic material with one or more fermenting microorganisms, wherein the
cellulosic
material is saccharified with an enzyme composition in the presence of the
polypeptide of
any of paragraphs 1-12.
[51] The method of paragraph 50, wherein the cellulosic material is pretreated
before
saccharification.
[52] The method of paragraph 50 or 51, wherein the enzyme composition
comprises
one or more (several) enzymes selected from the group consisting of a
cellulase, a GH61
polypeptide having cellulolytic enhancing activity, a hemicellulase, an
expansin, an esterase,
a laccase, a ligninolytic enzyme, a pectinase, a peroxidase, a protease, and a
swollenin.
[53] The method of paragraph 52, wherein the cellulase is one or more
(several)
enzymes selected from the group consisting of an endoglucanase, a
cellobiohydrolase, and
a beta-glucosidase.
[54] The method of paragraph 52, wherein the hemicellulase is one or more
(several)
enzymes selected from the group consisting of a xylanase, an acetyxylan
esterase, a feruloyl
esterase, an arabinofuranosidase, a xylosidase, and a glucuronidase.
[55] The method of any of paragraphs 50-54, wherein the fermenting of the
cellulosic
material produces a fermentation product.
[56] The method of any of paragraphs 55, further comprising recovering the
fermentation product from the fermentation.
[57] The method of paragraph 55 or 56, wherein the fermentation product is an
alcohol, an organic acid, a ketone, an amino acid, or a gas.
The invention described and claimed herein is not to be limited in scope by
the
specific aspects herein disclosed, since these aspects are intended as
illustrations of several
aspects of the invention. Any equivalent aspects are intended to be within the
scope of this
invention. Indeed, various modifications of the invention in addition to those
shown and
described herein will become apparent to those skilled in the art from the
foregoing
description. Such modifications are also intended to fall within the scope of
the appended
claims. In the case of conflict, the present disclosure including definitions
will control.
-80-
